Compositions for use in identification of bacteria

ABSTRACT

The present invention provides compositions, kits and methods for rapid identification and quantification of bacteria by molecular mass and base composition analysis.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 11/409,535, filed April 21, 2006, which is a continuation-in-part of U.S. application Ser. No. 11/060,135, filed Feb. 17, 2005 which claims the benefit of priority to U.S. Provisional Application Ser. No. 60/545,425 filed Feb. 18, 2004; U.S. Provisional Application Ser. No. 60/559,754, filed Apr. 5, 2004; U.S. Provisional Application Ser. No. 60/632,862, filed Dec. 3, 2004; U.S. Provisional Application Ser. No. 60/639,068, filed Dec. 22, 2004; and U.S. Provisional Application Ser. No. 60/648,188, filed Jan. 28, 2005. U.S. application Ser. No. 11/409,535 is a also continuation-in-part of U.S. application Ser. No. 10/728,486, filed Dec. 5, 2003 which claims the benefit of priority to U.S. Provisional Application Ser. No. 60/501,926, filed Sep. 11, 2003. U.S. application Ser. No. 11/409,535 also claims the benefit of priority to: U.S. Provisional Application Ser. No. 60/674,118, filed Apr. 21, 2005; U.S. Provisional Application Ser. No. 60/705,631, filed Aug. 3, 2005; U.S. Provisional Application Ser. No. 60/732,539, filed Nov. 1, 2005; and U.S. Provisional Application Ser. No. 60/773,124, filed Feb. 13, 2006. Each of the above-referenced U.S. Applications is incorporated herein by reference in its entirety. Methods disclosed in U.S. application Ser. Nos. 09/891,793, 10/156,608, 10/405,756, 10/418,514, 10/660,122, 10,660,996, 10/660,997, 10/660,998, 10/728,486, 11/060,135, and 11/073,362, are commonly owned and incorporated herein by reference in their entirety for any purpose.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with United States Government support under CDC contracts RO1 CI000099-01. The United States Government has certain rights in the invention.

SEQUENCE LISTING

The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled DIBIS0083USC3SEQ.txt, created on Mar. 6, 2007 which is 252 Kb in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention provides compositions, kits and methods for rapid identification and quantification of bacteria by molecular mass and base composition analysis.

BACKGROUND OF THE INVENTION

A problem in determining the cause of a natural infectious outbreak or a bioterrorist attack is the sheer variety of organisms that can cause human disease. There are over 1400 organisms infectious to humans; many of these have the potential to emerge suddenly in a natural epidemic or to be used in a malicious attack by bioterrorists (Taylor et al. Philos. Trans. R. Soc. London B. Biol. Sci., 2001, 356, 983-989). This number does not include numerous strain variants, bioengineered versions, or pathogens that infect plants or animals.

Much of the new technology being developed for detection of biological weapons incorporates a polymerase chain reaction (PCR) step based upon the use of highly specific primers and probes designed to selectively detect certain pathogenic organisms. Although this approach is appropriate for the most obvious bioterrorist organisms, like smallpox and anthrax, experience has shown that it is very difficult to predict which of hundreds of possible pathogenic organisms might be employed in a terrorist attack. Likewise, naturally emerging human disease that has caused devastating consequence in public health has come from unexpected families of bacteria, viruses, fungi, or protozoa. Plants and animals also have their natural burden of infectious disease agents and there are equally important biosafety and security concerns for agriculture.

A major conundrum in public health protection, biodefense, and agricultural safety and security is that these disciplines need to be able to rapidly identify and characterize infectious agents, while there is no existing technology with the breadth of function to meet this need. Currently used methods for identification of bacteria rely upon culturing the bacterium to effect isolation from other organisms and to obtain sufficient quantities of nucleic acid followed by sequencing of the nucleic acid, both processes which are time and labor intensive.

Mass spectrometry provides detailed information about the molecules being analyzed, including high mass accuracy. It is also a process that can be easily automated. DNA chips with specific probes can only determine the presence or absence of specifically anticipated organisms. Because there are hundreds of thousands of species of benign bacteria, some very similar in sequence to threat organisms, even arrays with 10,000 probes lack the breadth needed to identify a particular organism.

The present invention provides oligonucleotide primers and compositions and kits containing the oligonucleotide primers, which define bacterial bioagent identifying amplicons and, upon amplification, produce corresponding amplification products whose molecular masses provide the means to identify bacteria, for example, at and below the species taxonomic level.

SUMMARY OF THE INVENTION

The present invention provides compositions, kits and methods for rapid identification and quantification of bacteria by molecular mass and base composition analysis.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 456.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1261.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 456 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1261.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 288.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1269.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 288 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1269.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 698.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1420.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 698 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1420.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 217.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1167

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 217 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1167.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 399.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1041.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 399 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1041.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 430.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1321.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 430 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1321.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 174.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 853.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 174 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 853.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 172.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1360.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 172 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1360.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 456 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1261.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 456 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1261 and further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs: 288:1269, 698:1420, 217:1167, 399:1041, 430:1321, 174:853, and 172:1360.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 681.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1022.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 681 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1022.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 315.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1379.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 315 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1379.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 346.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 955.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 346 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 955.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 504.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1409.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 504 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1409.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 323.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1068.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 323 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1068.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 479.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 938.

Another embodiment is an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 479 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 938.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 681 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1022.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 681 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1022 and further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs: 315:1379, 346:955, 504:1409, 323:1068, 479:938.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 583.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 923.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 583 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 923.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 454.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1418.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 454 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1418.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 250.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 902.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 250 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 902.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 384.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 878.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 384 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 878.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 694.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1215.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 694 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1215.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 194.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1173.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 194 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1173.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 375.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 890.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 375 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 890.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 656.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1224.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 656 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1224.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 618.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1157.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 618 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1157.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 302.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 852.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 302 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 852.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 199.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 889.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 199 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 889.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 596.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1169.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 596 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1169.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 150.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1242.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 150 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1242.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 166.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1069.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 166 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1069.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 166.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1168.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 166 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1168.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 583 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 923 and further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs: 454:1418, 250:902, 384:878, 694:1215, 194:1173, 375:890, 656:1224, 618:1157, 302:852, 199:889, 596:1169, 150:1242, 166:1069 and 166:1168.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 437.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1137.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 437 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1137.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 530.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 891.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 530 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 891.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 474.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 869.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 474 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 869.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 268.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1284.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 268 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1284.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 418.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1301.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 418 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1301.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 318.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1300.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 318 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1300.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 440.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1076.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 440 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1076.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 219.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1013.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 219 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1013.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 437 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1137 and further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs: 530:891, 474:869, 268:1284, 418:1301, 318:1300, 440:1076 and 219:1013.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 325.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1163.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 325 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1163.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 278.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1039.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 278 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1039.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 465.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1037.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 465 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1037.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 148.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1172.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 148 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1172.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 190.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1254.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 190 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1254.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 266.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1094.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 266 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1094.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 508.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1297.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 508 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1297.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 259.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1060.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 259 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1060.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 325 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1163 and further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs: 278:1039: 465:1037, 148:1172, 190:1254, 266:1094, 508:1297 and 259:1060.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 376.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1265.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 376 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1265.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 267.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1341.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 267 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1341.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 705.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1056.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 705 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1056.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 710.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1259.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 710 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1259.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 374.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1111.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 374 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1111.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 545.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 978.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 545 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 978.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 249.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1095.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 249 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1095.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 195.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1376.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 195 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1376.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 311.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1014.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 311 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1014.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 365.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1052.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 365 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1052.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 527.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1071.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 527 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1071.

One embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 490.

Another embodiment is an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1182.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 490 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1182.

Another embodiment is a kit comprising an oligonucleotide primer pair including an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 376 and an oligonucleotide primer 14 to 35 nucleobases in length having at least 70% sequence identity with SEQ ID NO: 1265 and further comprising one or more primer pairs wherein each member of said one or more primer pairs is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by SEQ ID NOs: 267:1341, 705:1056, 710:1259, 374:1111, 545:978, 249:1095, 195:1376, 311:1014, 365:1052, 527:1071 and 490:1182.

In some embodiments, either or both of the primers of a primer pair composition contain at least one modified nucleobase such as 5-propynyluracil or 5-propynylcytosine for example.

In some embodiments, either or both of the primers of the primer pair comprises at least one universal nucleobase such as inosine for example.

In some embodiments, either or both of the primers of the primer pair comprises at least one non-templated T residue on the 5′-end.

In some embodiments, either or both of the primers of the primer pair comprises at least one non-template tag.

In some embodiments, either or both of the primers of the primer pair comprises at least one molecular mass modifying tag.

In some embodiments, the present invention provides primers and compositions comprising pairs of primers, and kits containing the same, and methods for use in identification of bacteria. The primers are designed to produce amplification products of DNA encoding genes that have conserved and variable regions across different subgroups and genotypes of bacteria.

Some embodiments are kits that contain one or more of the primer pair compositions. In some embodiments, each member of the one or more primer pairs of the kit is of a length of 14 to 35 nucleobases and has 70% to 100% sequence identity with the corresponding member from any of the primer pairs listed in Table 2.

Some embodiments of the kits contain at least one calibration polynucleotide for use in quantitiation of bacteria in a given sample, and also for use as a positive control for amplification.

Some embodiments of the kits contain at least one anion exchange functional group linked to a magnetic bead.

In some embodiments, the present invention also provides methods for identification of bacteria. Nucleic acid from the bacterium is amplified using the primers described above to obtain an amplification product. The molecular mass of the amplification product is measured. Optionally, the base composition of the amplification product is determined from the molecular mass. The molecular mass or base composition is compared with a plurality of molecular masses or base compositions of known analogous bacterial identifying amplicons, wherein a match between the molecular mass or base composition and a member of the plurality of molecular masses or base compositions identifies the bacterium. In some embodiments, the molecular mass is measured by mass spectrometry in a modality such as electrospray ionization (ESI) time of flight (TOF) mass spectrometry or ESI Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, for example. Other mass spectrometry techniques can also be used to measure the molecular mass of bacterial bioagent identifying amplicons.

In some embodiments, the present invention is also directed to a method for determining the presence or absence of a bacterium in a sample. Nucleic acid from the sample is amplified using the composition described above to obtain an amplification product. The molecular mass of the amplification product is determined. Optionally, the base composition of the amplification product is determined from the molecular mass. The molecular mass or base composition of the amplification product is compared with the known molecular masses or base compositions of one or more known analogous bacterial bioagent identifying amplicons, wherein a match between the molecular mass or base composition of the amplification product and the molecular mass or base composition of one or more known bacterial bioagent identifying amplicons indicates the presence of the bacterium in the sample. In some embodiments, the molecular mass is measured by mass spectrometry.

In some embodiments, the present invention also provides methods for determination of the quantity of an unknown bacterium in a sample. The sample is contacted with the composition described above and a known quantity of a calibration polynucleotide comprising a calibration sequence. Nucleic acid from the unknown bacterium in the sample is concurrently amplified with the composition described above and nucleic acid from the calibration polynucleotide in the sample is concurrently amplified with the composition described above to obtain a first amplification product comprising a bacterial bioagent identifying amplicon and a second amplification product comprising a calibration amplicon. The molecular masses and abundances for the bacterial bioagent identifying amplicon and the calibration amplicon are determined. The bacterial bioagent identifying amplicon is distinguished from the calibration amplicon based on molecular mass and comparison of bacterial bioagent identifying amplicon abundance and calibration amplicon abundance indicates the quantity of bacterium in the sample. In some embodiments, the base composition of the bacterial bioagent identifying amplicon is determined.

In some embodiments, the present invention provides methods for detecting or quantifying bacteria by combining a nucleic acid amplification process with a mass determination process. In some embodiments, such methods identify or otherwise analyze the bacterium by comparing mass information from an amplification product with a calibration or control product. Such methods can be carried out in a highly multiplexed and/or parallel manner allowing for the analysis of as many as 300 samples per 24 hours on a single mass measurement platform. The accuracy of the mass determination methods in some embodiments of the present invention permits allows for the ability to discriminate between different bacteria such as, for example, various genotypes and drug resistant strains of Staphylococcus aureus.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing summary of the invention, as well as the following detailed description of the invention, is better understood when read in conjunction with the accompanying drawings which are included by way of example and not by way of limitation.

FIG. 1: process diagram illustrating a representative primer pair selection process.

FIG. 2: process diagram illustrating an embodiment of the calibration method.

FIG. 3: common pathogenic bacteria and primer pair coverage. The primer pair number in the upper right hand corner of each polygon indicates that the primer pair can produce a bioagent identifying amplicon for all species within that polygon.

FIG. 4: a representative 3D diagram of base composition (axes A, G and C) of bioagent identifying amplicons obtained with primer pair number 14 (a precursor of primer pair number 348 which targets 16S rRNA). The diagram indicates that the experimentally determined base compositions of the clinical samples (labeled NHRC samples) closely match the base compositions expected for Streptococcus pyogenes and are distinct from the expected base compositions of other organisms.

FIG. 5: a representative mass spectrum of amplification products indicating the presence of bioagent identifying amplicons of Streptococcus pyogenes, Neisseria meningitidis, and Haemophilus influenzae obtained from amplification of nucleic acid from a clinical sample with primer pair number 349 which targets 23S rRNA. Experimentally determined molecular masses and base compositions for the sense strand of each amplification product are shown.

FIG. 6: a representative mass spectrum of amplification products representing a bioagent identifying amplicon of Streptococcus pyogenes, and a calibration amplicon obtained from amplification of nucleic acid from a clinical sample with primer pair number 356 which targets rplB. The experimentally determined molecular mass and base composition for the sense strand of the Streptococcus pyogenes amplification product is shown.

FIG. 7: a representative mass spectrum of an amplified nucleic acid mixture which contained the Ames strain of Bacillus anthracis, a known quantity of combination calibration polynucleotide (SEQ ID NO: 1464), and primer pair number 350 which targets the capC gene on the virulence plasmid pX02 of Bacillus anthracis. Calibration amplicons produced in the amplification reaction are visible in the mass spectrum as indicated and abundance data (peak height) are used to calculate the quantity of the Ames strain of Bacillus anthracis.

DEFINITIONS

As used herein, the term “abundance” refers to an amount. The amount may be described in terms of concentration which are common in molecular biology such as “copy number,” “pfu” or plate-forming unit” which are well known to those with ordinary skill. Concentration may be relative to a known standard or may be absolute.

As used herein, the term “amplifiable nucleic acid” is used in reference to nucleic acids that may be amplified by any amplification method. It is contemplated that “amplifiable nucleic acid” also comprises “sample template.”

As used herein the term “amplification” refers to a special case of nucleic acid replication involving template specificity. It is to be contrasted with non-specific template replication (i.e., replication that is template-dependent but not dependent on a specific template). Template specificity is here distinguished from fidelity of replication (i.e., synthesis of the proper polynucleotide sequence) and nucleotide (ribo- or deoxyribo-) specificity. Template specificity is frequently described in terms of “target” specificity. Target sequences are “targets” in the sense that they are sought to be sorted out from other nucleic acid. Amplification techniques have been designed primarily for this sorting out. Template specificity is achieved in most amplification techniques by the choice of enzyme. Amplification enzymes are enzymes that, under conditions they are used, will process only specific sequences of nucleic acid in a heterogeneous mixture of nucleic acid. For example, in the case of Qβ replicase, MDV-1 RNA is the specific template for the replicase (D. L. Kacian et al., Proc. Natl. Acad. Sci. USA 69:3038 [1972]). Other nucleic acid will not be replicated by this amplification enzyme. Similarly, in the case of T7 RNA polymerase, this amplification enzyme has a stringent specificity for its own promoters (Chamberlin et al., Nature 228:227 [1970]). In the case of T4 DNA ligase, the enzyme will not ligate the two oligonucleotides or polynucleotides, where there is a mismatch between the oligonucleotide or polynucleotide substrate and the template at the ligation junction (D. Y. Wu and R. B. Wallace, Genomics 4:560 [1989]). Finally, Taq and Pfu polymerases, by virtue of their ability to function at high temperature, are found to display high specificity for the sequences bounded and thus defined by the primers; the high temperature results in thermodynamic conditions that favor primer hybridization with the target sequences and not hybridization with non-target sequences (H. A. Erlich (ed.), PCR Technology, Stockton Press [1989]).

As used herein, the term “amplification reagents” refers to those reagents (deoxyribonucleotide triphosphates, buffer, etc.), needed for amplification, excluding primers, nucleic acid template, and the amplification enzyme. Typically, amplification reagents along with other reaction components are placed and contained in a reaction vessel (test tube, microwell, etc.).

As used herein, the term “analogous” when used in context of comparison of bioagent identifying amplicons indicates that the bioagent identifying amplicons being compared are produced with the same pair of primers. For example, bioagent identifying amplicon “A” and bioagent identifying amplicon “B”, produced with the same pair of primers are analogous with respect to each other. Bioagent identifying amplicon “C”, produced with a different pair of primers is not analogous to either bioagent identifying amplicon “A” or bioagent identifying amplicon “B”.

As used herein, the term “anion exchange functional group” refers to a positively charged functional group capable of binding an anion through an electrostatic interaction. The most well known anion exchange functional groups are the amines, including primary, secondary, tertiary and quaternary amines.

The term “bacteria” or “bacterium” refers to any member of the groups of eubacteria and archaebacteria.

As used herein, a “base composition” is the exact number of each nucleobase (for example, A, T, C and G) in a segment of nucleic acid. For example, amplification of nucleic acid of Staphylococcus aureus strain carrying the lukS-PV gene with primer pair number 2095 (SEQ ID NOs: 456:1261) produces an amplification product 117 nucleobases in length from nucleic acid of the lukS-PV gene that has a base composition of A35 G17 C19 T46 (by convention - with reference to the sense strand of the amplification product). Because the molecular masses of each of the four natural nucleotides and chemical modifications thereof are known (if applicable), a measured molecular mass can be deconvoluted to a list of possible base compositions. Identification of a base composition of a sense strand which is complementary to the corresponding antisense strand in terms of base composition provides a confirmation of the true base composition of an unknown amplification product. For example, the base composition of the antisense strand of the 139 nucleobase amplification product described above is A46 G19 C17 T35.

As used herein, a “base composition probability cloud” is a representation of the diversity in base composition resulting from a variation in sequence that occurs among different isolates of a given species. The “base composition probability cloud” represents the base composition constraints for each species and is typically visualized using a pseudo four-dimensional plot.

In the context of this invention, a “bioagent” is any organism, cell, or virus, living or dead, or a nucleic acid derived from such an organism, cell or virus. Examples of bioagents include, but are not limited, to cells, (including but not limited to human clinical samples, bacterial cells and other pathogens), viruses, fungi, protists, parasites, and pathogenicity markers (including but not limited to: pathogenicity islands, antibiotic resistance genes, virulence factors, toxin genes and other bioregulating compounds). Samples may be alive or dead or in a vegetative state (for example, vegetative bacteria or spores) and may be encapsulated or bioengineered. In the context of this invention, a “pathogen” is a bioagent which causes a disease or disorder.

As used herein, a “bioagent division” is defined as group of bioagents above the species level and includes but is not limited to, orders, families, classes, clades, genera or other such groupings of bioagents above the species level.

As used herein, the term “bioagent identifying amplicon” refers to a polynucleotide that is amplified from a bioagent in an amplification reaction and which 1) provides sufficient variability to distinguish among bioagents from whose nucleic acid the bioagent identifying amplicon is produced and 2) whose molecular mass is amenable to a rapid and convenient molecular mass determination modality such as mass spectrometry, for example.

As used herein, the term “biological product” refers to any product originating from an organism. Biological products are often products of processes of biotechnology. Examples of biological products include, but are not limited to: cultured cell lines, cellular components, antibodies, proteins and other cell-derived biomolecules, growth media, growth harvest fluids, natural products and bio-pharmaceutical products.

The terms “biowarfare agent” and “bioweapon” are synonymous and refer to a bacterium, virus, fungus or protozoan that could be deployed as a weapon to cause bodily harm to individuals. Military or terrorist groups may be implicated in deployment of biowarfare agents.

In context of this invention, the term “broad range survey primer pair” refers to a primer pair designed to produce bioagent identifying amplicons across different broad groupings of bioagents. For example, the ribosomal RNA-targeted primer pairs are broad range survey primer pairs which have the capability of producing bacterial bioagent identifying amplicons for essentially all known bacteria. With respect to broad range primer pairs employed for identification of bacteria, a broad range survey primer pair for bacteria such as 16S rRNA primer pair number 346 (SEQ ID NOs: 202:1110) for example, will produce an bacterial bioagent identifying amplicon for essentially all known bacteria.

The term “calibration amplicon” refers to a nucleic acid segment representing an amplification product obtained by amplification of a calibration sequence with a pair of primers designed to produce a bioagent identifying amplicon.

The term “calibration sequence” refers to a polynucleotide sequence to which a given pair of primers hybridizes for the purpose of producing an internal (i.e: included in the reaction) calibration standard amplification product for use in determining the quantity of a bioagent in a sample. The calibration sequence may be expressly added to an amplification reaction, or may already be present in the sample prior to analysis.

The term “clade primer pair” refers to a primer pair designed to produce bioagent identifying amplicons for species belonging to a clade group. A clade primer pair may also be considered as a “speciating” primer pair which is useful for distinguishing among closely related species.

The term “codon” refers to a set of three adjoined nucleotides (triplet) that codes for an amino acid or a termination signal.

In context of this invention, the term “codon base composition analysis,” refers to determination of the base composition of an individual codon by obtaining a bioagent identifying amplicon that includes the codon. The bioagent identifying amplicon will at least include regions of the target nucleic acid sequence to which the primers hybridize for generation of the bioagent identifying amplicon as well as the codon being analyzed, located between the two primer hybridization regions.

As used herein, the terms “complementary” or “complementarity” are used in reference to polynucleotides (i.e., a sequence of nucleotides such as an oligonucleotide or a target nucleic acid) related by the base-pairing rules. For example, for the sequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods that depend upon binding between nucleic acids. Either term may also be used in reference to individual nucleotides, especially within the context of polynucleotides. For example, a particular nucleotide within an oligonucleotide may be noted for its complementarity, or lack thereof, to a nucleotide within another nucleic acid strand, in contrast or comparison to the complementarity between the rest of the oligonucleotide and the nucleic acid strand.

The term “complement of a nucleic acid sequence” as used herein refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5′ end of one sequence is paired with the 3′ end of the other, is in “antiparallel association.” Certain bases not commonly found in natural nucleic acids may be included in the nucleic acids of the present invention and include, for example, inosine and 7-deazaguanine. Complementarity need not be perfect; stable duplexes may contain mismatched base pairs or unmatched bases. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the oligonucleotide, ionic strength and incidence of mismatched base pairs. Where a first oligonucleotide is complementary to a region of a target nucleic acid and a second oligonucleotide has complementary to the same region (or a portion of this region) a “region of overlap” exists along the target nucleic acid. The degree of overlap will vary depending upon the extent of the complementarity.

In context of this invention, the term “division-wide primer pair” refers to a primer pair designed to produce bioagent identifying amplicons within sections of a broader spectrum of bioagents For example, primer pair number 352 (SEQ ID NOs: 687:1411), a division-wide primer pair, is designed to produce bacterial bioagent identifying amplicons for members of the Bacillus group of bacteria which comprises, for example, members of the genera Streptococci, Enterococci, and Staphylococci. Other division-wide primer pairs may be used to produce bacterial bioagent identifying amplicons for other groups of bacterial bioagents.

As used herein, the term “concurrently amplifying” used with respect to more than one amplification reaction refers to the act of simultaneously amplifying more than one nucleic acid in a single reaction mixture.

As used herein, the term “drill-down primer pair” refers to a primer pair designed to produce bioagent identifying amplicons for identification of sub-species characteristics or confirmation of a species assignment. For example, primer pair number 2146 (SEQ ID NOs: 437:1137), a drill-down Staphylococcus aureus genotyping primer pair, is designed to produce Staphylococcus aureus genotyping amplicons. Other drill-down primer pairs may be used to produce bioagent identifying amplicons for Staphylococcus aureus and other bacterial species.

The term “duplex” refers to the state of nucleic acids in which the base portions of the nucleotides on one strand are bound through hydrogen bonding the their complementary bases arrayed on a second strand. The condition of being in a duplex form reflects on the state of the bases of a nucleic acid. By virtue of base pairing, the strands of nucleic acid also generally assume the tertiary structure of a double helix, having a major and a minor groove. The assumption of the helical form is implicit in the act of becoming duplexed.

As used herein, the term “etiology” refers to the causes or origins, of diseases or abnormal physiological conditions.

The term “gene” refers to a DNA sequence that comprises control and coding sequences necessary for the production of an RNA having a non-coding function (e.g., a ribosomal or transfer RNA), a polypeptide or a precursor. The RNA or polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or function is retained.

The terms “homology,” “homologous” and “sequence identity” refer to a degree of identity. There may be partial homology or complete homology. A partially homologous sequence is one that is less than 100% identical to another sequence. Determination of sequence identity is described in the following example: a primer 20 nucleobases in length which is otherwise identical to another 20 nucleobase primer but having two non-identical residues has 18 of 20 identical residues (18/20=0.9 or 90% sequence identity). In another example, a primer 15 nucleobases in length having all residues identical to a 15 nucleobase segment of a primer 20 nucleobases in length would have 15/20=0.75 or 75% sequence identity with the 20 nucleobase primer. In context of the present invention, sequence identity is meant to be properly determined when the query sequence and the subject sequence are both described and aligned in the 5′ to 3′ direction. Sequence alignment algorithms such as BLAST, will return results in two different alignment orientations. In the Plus/Plus orientation, both the query sequence and the subject sequence are aligned in the 5′ to 3′ direction. On the other hand, in the Plus/Minus orientation, the query sequence is in the 5′ to 3′ direction while the subject sequence is in the 3′ to 5′ direction. It should be understood that with respect to the primers of the present invention, sequence identity is properly determined when the alignment is designated as Plus/Plus. Sequence identity may also encompass alternate or modified nucleobases that perform in a functionally similar manner to the regular nucleobases adenine, thymine, guanine and cytosine with respect to hybridization and primer extension in amplification reactions. In a non-limiting example, if the 5-propynyl pyrimidines propyne C and/or propyne T replace one or more C or T residues in one primer which is otherwise identical to another primer in sequence and length, the two primers will have 100% sequence identity with each other. In another non-limiting example, Inosine (I) may be used as a replacement for G or T and effectively hybridize to C, A or U (uracil). Thus, if inosine replaces one or more C, A or U residues in one primer which is otherwise identical to another primer in sequence and length, the two primers will have 100% sequence identity with each other. Other such modified or universal bases may exist which would perform in a functionally similar manner for hybridization and amplification reactions and will be understood to fall within this definition of sequence identity.

As used herein, “housekeeping gene” refers to a gene encoding a protein or RNA involved in basic functions required for survival and reproduction of a bioagent. Housekeeping genes include, but are not limited to genes encoding RNA or proteins involved in translation, replication, recombination and repair, transcription, nucleotide metabolism, amino acid metabolism, lipid metabolism, energy generation, uptake, secretion and the like.

As used herein, the term “hybridization” is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is influenced by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, and the T_(m) of the formed hybrid. “Hybridization” methods involve the annealing of one nucleic acid to another, complementary nucleic acid, i.e., a nucleic acid having a complementary nucleotide sequence. The ability of two polymers of nucleic acid containing complementary sequences to find each other and anneal through base pairing interaction is a well-recognized phenomenon. The initial observations of the “hybridization” process by Marmur and Lane, Proc. Natl. Acad. Sci. USA 46:453 (1960) and Doty et al., Proc. Natl. Acad. Sci. USA 46:461 (1960) have been followed by the refinement of this process into an essential tool of modern biology.

The term “in silico” refers to processes taking place via computer calculations. For example, electronic PCR (ePCR) is a process analogous to ordinary PCR except that it is carried out using nucleic acid sequences and primer pair sequences stored on a computer formatted medium.

As used herein, “intelligent primers” are primers that are designed to bind to highly conserved sequence regions of a bioagent identifying amplicon that flank an intervening variable region and, upon amplification, yield amplification products which ideally provide enough variability to distinguish individual bioagents, and which are amenable to molecular mass analysis. By the term “highly conserved,” it is meant that the sequence regions exhibit between about 80-100%, or between about 90-100%, or between about 95-100% identity among all, or at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of species or strains.

The “ligase chain reaction” (LCR; sometimes referred to as “Ligase Amplification Reaction” (LAR) described by Barany, Proc. Natl. Acad. Sci., 88:189 (1991); Barany, PCR Methods and Applic., 1:5 (1991); and Wu and Wallace, Genomics 4:560 (1989) has developed into a well-recognized alternative method for amplifying nucleic acids. In LCR, four oligonucleotides, two adjacent oligonucleotides which uniquely hybridize to one strand of target DNA, and a complementary set of adjacent oligonucleotides, that hybridize to the opposite strand are mixed and DNA ligase is added to the mixture. Provided that there is complete complementarity at the junction, ligase will covalently link each set of hybridized molecules. Importantly, in LCR, two probes are ligated together only when they base-pair with sequences in the target sample, without gaps or mismatches. Repeated cycles of denaturation, hybridization and ligation amplify a short segment of DNA. LCR has also been used in combination with PCR to achieve enhanced detection of single-base changes. However, because the four oligonucleotides used in this assay can pair to form two short ligatable fragments, there is the potential for the generation of target-independent background signal. The use of LCR for mutant screening is limited to the examination of specific nucleic acid positions.

The term “locked nucleic acid” or “LNA” refers to a nucleic acid analogue containing one or more 2′-O, 4′-C-methylene-p-D-ribofuranosyl nucleotide monomers in an RNA mimicking sugar conformation. LNA oligonucleotides display unprecedented hybridization affinity toward complementary single-stranded RNA and complementary single- or double-stranded DNA. LNA oligonucleotides induce A-type (RNA-like) duplex conformations. The primers of the present invention may contain LNA modifications.

As used herein, the term “mass-modifying tag” refers to any modification to a given nucleotide which results in an increase in mass relative to the analogous non-mass modified nucleotide. Mass-modifying tags can include heavy isotopes of one or more elements included in the nucleotide such as carbon-13 for example. Other possible modifications include addition of substituents such as iodine or bromine at the 5 position of the nucleobase for example.

The term “mass spectrometry” refers to measurement of the mass of atoms or molecules. The molecules are first converted to ions, which are separated using electric or magnetic fields according to the ratio of their mass to electric charge. The measured masses are used to identity the molecules.

The term “microorganism” as used herein means an organism too small to be observed with the unaided eye and includes, but is not limited to bacteria, virus, protozoans, fingi; and ciliates.

The term “multi-drug resistant” or multiple-drug resistant“refers to a microorganism which is resistant to more than one of the antibiotics or antimicrobial agents used in the treatment of said microorganism.

The term “multiplex PCR” refers to a PCR reaction where more than one primer set is included in the reaction pool allowing 2 or more different DNA targets to be amplified by PCR in a single reaction tube.

The term “non-template tag” refers to a stretch of at least three guanine or cytosine nucleobases of a primer used to produce a bioagent identifying amplicon which are not complementary to the template. A non-template tag is incorporated into a primer for the purpose of increasing the primer-duplex stability of later cycles of amplification by incorporation of extra G-C pairs which each have one additional hydrogen bond relative to an A-T pair.

The term “nucleic acid sequence” as used herein refers to the linear composition of the nucleic acid residues A, T, C or G or any modifications thereof, within an oligonucleotide, nucleotide or polynucleotide, and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin which may be single or double stranded, and represent the sense or antisense strand

As used herein, the term “nucleobase” is synonymous with other terms in use in the art including “nucleotide,” “deoxynucleotide,” “nucleotide residue,” “deoxynucleotide residue,” “nucleotide triphosphate (NTP),” or deoxynucleotide triphosphate (dNTP).

The term “nucleotide analog” as used herein refers to modified or non-naturally occurring nucleotides such as 5-propynyl pyrimidines (i.e., 5-propynyl-dTTP and 5-propynyl-dTCP), 7-deaza purines (i.e., 7-deaza-dATP and 7-deaza-dGTP). Nucleotide analogs include base analogs and comprise modified forms of deoxyribonucleotides as well as ribonucleotides.

The term “oligonucleotide” as used herein is defined as a molecule comprising two or more deoxyribonucleotides or ribonucleotides, preferably at least 5 nucleotides, more preferably at least about 13 to 35 nucleotides. The exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. The oligonucleotide may be generated in any manner, including chemical synthesis, DNA replication, reverse transcription, PCR, or a combination thereof. Because mononucleotides are reacted to make oligonucleotides in a manner such that the 5′ phosphate of one mononucleotide pentose ring is attached to the 3′ oxygen of its neighbor in one direction via a phosphodiester linkage, an end of an oligonucleotide is referred to as the “5′-end” if its 5′ phosphate is not linked to the 3′ oxygen of a mononucleotide pentose ring and as the “3′-end” if its 3′ oxygen is not linked to a 5′ phosphate of a subsequent mononucleotide pentose ring. As used herein, a nucleic acid sequence, even if internal to a larger oligonucleotide, also may be said to have 5′ and 3′ ends. A first region along a nucleic acid strand is said to be upstream of another region if the 3′ end of the first region is before the 5′ end of the second region when moving along a strand of nucleic acid in a 5′ to 3′ direction. All oligonucleotide primers disclosed herein are understood to be presented in the 5′ to 3′ direction when reading left to right. When two different, non-overlapping oligonucleotides anneal to different regions of the same linear complementary nucleic acid sequence, and the 3′ end of one oligonucleotide points towards the 5′ end of the other, the former may be called the “upstream” oligonucleotide and the latter the “downstream” oligonucleotide. Similarly, when two overlapping oligonucleotides are hybridized to the same linear complementary nucleic acid sequence, with the first oligonucleotide positioned such that its 5′ end is upstream of the 5′ end of the second oligonucleotide, and the 3′ end of the first oligonucleotide is upstream of the 3′ end of the second oligonucleotide, the first oligonucleotide may be called the “upstream” oligonucleotide and the second oligonucleotide may be called the “downstream” oligonucleotide.

In the context of this invention, a “pathogen” is a bioagent which causes a disease or disorder.

As used herein, the terms “PCR product,” “PCR fragment,” and “amplification product” refer to the resultant mixture of compounds after two or more cycles of the PCR steps of denaturation, annealing and extension are complete. These terms encompass the case where there has been amplification of one or more segments of one or more target sequences.

The term “peptide nucleic acid” (“PNA”) as used herein refers to a molecule comprising bases or base analogs such as would be found in natural nucleic acid, but attached to a peptide backbone rather than the sugar-phosphate backbone typical of nucleic acids. The attachment of the bases to the peptide is such as to allow the bases to base pair with complementary bases of nucleic acid in a manner similar to that of an oligonucleotide. These small molecules, also designated anti gene agents, stop transcript elongation by binding to their complementary strand of nucleic acid (Nielsen, et al. Anticancer Drug Des. 8:53 63). The primers of the present invention may comprise PNAs.

The term “polymerase” refers to an enzyme having the ability to synthesize a complementary strand of nucleic acid from a starting template nucleic acid strand and free dNTPs.

As used herein, the term “polymerase chain reaction” (“PCR”) refers to the method of K. B. Mullis U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,965,188, hereby incorporated by reference, that describe a method for increasing the concentration of a segment of a target sequence in a mixture of genomic DNA without cloning or purification. This process for amplifying the target sequence consists of introducing a large excess of two oligonucleotide primers to the DNA mixture containing the desired target sequence, followed by a precise sequence of thermal cycling in the presence of a DNA polymerase. The two primers are complementary to their respective strands of the double stranded target sequence. To effect amplification, the mixture is denatured and the primers then annealed to their complementary sequences within the target molecule. Following annealing, the primers are extended with a polymerase so as to form a new pair of complementary strands. The steps of denaturation, primer annealing, and polymerase extension can be repeated many times (i.e., denaturation, annealing and extension constitute one “cycle”; there can be numerous “cycles”) to obtain a high concentration of an amplified segment of the desired target sequence. The length of the amplified segment of the desired target sequence is determined by the relative positions of the primers with respect to each other, and therefore, this length is a controllable parameter. By virtue of the repeating aspect of the process, the method is referred to as the “polymerase chain reaction” (hereinafter “PCR”). Because the desired amplified segments of the target sequence become the predominant sequences (in terms of concentration) in the mixture, they are said to be “PCR amplified.” With PCR, it is possible to amplify a single copy of a specific target sequence in genomic DNA to a level detectable by several different methodologies (e.g., hybridization with a labeled probe; incorporation of biotinylated primers followed by avidin-enzyme conjugate detection; incorporation of 32P-labeled deoxynucleotide triphosphates, such as dCTP or dATP, into the amplified segment). In addition to genomic DNA, any oligonucleotide or polynucleotide sequence can be amplified with the appropriate set of primer molecules. In particular, the amplified segments created by the PCR process itself are, themselves, efficient templates for subsequent PCR amplifications.

The term “polymerization means” or “polymerization agent” refers to any agent capable of facilitating the addition of nucleoside triphosphates to an oligonucleotide. Preferred polymerization means comprise DNA and RNA polymerases.

As used herein, the terms “pair of primers,” or “primer pair” are synonymous. A primer pair is used for amplification of a nucleic acid sequence. A pair of primers comprises a forward primer and a reverse primer. The forward primer hybridizes to a sense strand of a target gene sequence to be amplified and primes synthesis of an antisense strand (complementary to the sense strand) using the target sequence as a template. A reverse primer hybridizes to the antisense strand of a target gene sequence to be amplified and primes synthesis of a sense strand (complementary to the antisense strand) using the target sequence as a template.

The primers are designed to bind to highly conserved sequence regions of a bioagent identifying amplicon that flank an intervening variable region and yield amplification products which ideally provide enough variability to distinguish each individual bioagent, and which are amenable to molecular mass analysis. In some embodiments, the highly conserved sequence regions exhibit between about 80-100%, or between about 90-100%, or between about 95-100% identity, or between about 99-100% identity. The molecular mass of a given amplification product provides a means of identifying the bioagent from which it was obtained, due to the variability of the variable region. Thus design of the primers requires selection of a variable region with appropriate variability to resolve the identity of a given bioagent. Bioagent identifying amplicons are ideally specific to the identity of the bioagent.

Properties of the primers may include any number of properties related to structure including, but not limited to: nucleobase length which may be contiguous (linked together) or non-contiguous (for example, two or more contiguous segments which are joined by a linker or loop moiety), modified or universal nucleobases (used for specific purposes such as for example, increasing hybridization affinity, preventing non-templated adenylation and modifying molecular mass) percent complementarity to a given target sequences.

Properties of the primers also include functional features including, but not limited to, orientation of hybridization (forward or reverse) relative to a nucleic acid template. The coding or sense strand is the strand to which the forward priming primer hybridizes (forward priming orientation) while the reverse priming primer hybridizes to the non-coding or antisense strand (reverse priming orientation). The functional properties of a given primer pair also include the generic template nucleic acid to which the primer pair hybridizes. For example, identification of bioagents can be accomplished at different levels using primers suited to resolution of each individual level of identification. Broad range survey primers are designed with the objective of identifying a bioagent as a member of a particular division (e.g., an order, family, genus or other such grouping of bioagents above the species level of bioagents). In some embodiments, broad range survey intelligent primers are capable of identification of bioagents at the species or sub-species level. Other primers may have the functionality of producing bioagent identifying amplicons for members of a given taxonomic genus, clade, species, sub-species or genotype (including genetic variants which may include presence of virulence genes or antibiotic resistance genes or mutations). Additional functional properties of primer pairs include the functionality of performing amplification either singly (single primer pair per amplification reaction vessel) or in a multiplex fashion (multiple primer pairs and multiple amplification reactions within a single reaction vessel).

As used herein, the terms “purified” or “substantially purified” refer to molecules, either nucleic or amino acid sequences, that are removed from their natural environment, isolated or separated, and are at least 60% free, preferably 75% free, and most preferably 90% free from other components with which they are naturally associated. An “isolated polynucleotide” or “isolated oligonucleotide” is therefore a substantially purified polynucleotide.

The term “reverse transcriptase” refers to an enzyme having the ability to transcribe DNA from an RNA template. This enzymatic activity is known as reverse transcriptase activity. Reverse transcriptase activity is desirable in order to obtain DNA from RNA viruses which can then be amplified and analyzed by the methods of the present invention.

The term “ribosomal RNA” or “rRNA” refers to the primary ribonucleic acid constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of cells and exist in the cytoplasm. Ribosomal RNAs are transcribed from the DNA genes encoding them.

The term “sample” in the present specification and claims is used in its broadest sense. On the one hand it is meant to include a specimen or culture (e.g., microbiological cultures). On the other hand, it is meant to include both biological and environmental samples. A sample may include a specimen of synthetic origin. Biological samples may be animal, including human, fluid, solid (e.g., stool) or tissue, as well as liquid and solid food and feed products and ingredients such as dairy items, vegetables, meat and meat by-products, and waste. Biological samples may be obtained from all of the various families of domestic animals, as well as feral or wild animals, including, but not limited to, such animals as ungulates, bear, fish, lagamorphs, rodents, etc. Environmental samples include environmental material such as surface matter, soil, water, air and industrial samples, as well as samples obtained from food and dairy processing instruments, apparatus, equipment, utensils, disposable and non-disposable items. These examples are not to be construed as limiting the sample types applicable to the present invention. The term “source of target nucleic acid” refers to any sample that contains nucleic acids (RNA or DNA). Particularly preferred sources of target nucleic acids are biological samples including, but not limited to blood, saliva, cerebral spinal fluid, pleural fluid, milk, lymph, sputum and semen.

As used herein, the term “sample template” refers to nucleic acid originating from a sample that is analyzed for the presence of “target” (defined below). In contrast, “background template” is used in reference to nucleic acid other than sample template that may or may not be present in a sample. Background template is often a contaminant. It may be the result of carryover, or it may be due to the presence of nucleic acid contaminants sought to be purified away from the sample. For example, nucleic acids from organisms other than those to be detected may be present as background in a test sample.

A “segment” is defined herein as a region of nucleic acid within a target sequence.

The “self-sustained sequence replication reaction” (3SR) (Guatelli et al., Proc. Natl. Acad. Sci., 87:1874-1878 [1990], with an erratum at Proc. Natl. Acad. Sci., 87:7797 [1990]) is a transcription-based in vitro amplification system (Kwok et al., Proc. Natl. Acad. Sci., 86:1173-1177 [1989]) that can exponentially amplify RNA sequences at a uniform temperature. The amplified RNA can then be utilized for mutation detection (Fahy et al., PCR Meth. Appl., 1:25-33 [1991]). In this method, an oligonucleotide primer is used to add a phage RNA polymerase promoter to the 5′ end of the sequence of interest. In a cocktail of enzymes and substrates that includes a second primer, reverse transcriptase, RNase H, RNA polymerase and ribo- and deoxyribonucleoside triphosphates, the target sequence undergoes repeated rounds of transcription, cDNA synthesis and second-strand synthesis to amplify the area of interest. The use of 3SR to detect mutations is kinetically limited to screening small segments of DNA (e.g., 200-300 base pairs).

As used herein, the term “sequence alignment” refers to a listing of multiple DNA or amino acid sequences and aligns them to highlight their similarities. The listings can be made using bioinformatics computer programs.

In context of this invention, the term “speciating primer pair” refers to a primer pair designed to produce a bioagent identifying amplicon with the diagnostic capability of identifying species members of a group of genera or a particular genus of bioagents. Primer pair number 2249 (SEQ ID NOs: 430:1321), for example, is a speciating primer pair used to distinguish Staphylococcus aureus from other species of the genus Staphylococcus.

As used herein, a “sub-species characteristic” is a genetic characteristic that provides the means to distinguish two members of the same bioagent species. For example, one viral strain could be distinguished from another viral strain of the same species by possessing a genetic change (e.g., for example, a nucleotide deletion, addition or substitution) in one of the viral genes, such as the RNA-dependent RNA polymerase. Sub-species characteristics such as virulence genes and drug-are responsible for the phenotypic differences among the different strains of bacteria.

As used herein, the term “target” is used in a broad sense to indicate the gene or genomic region being amplified by the primers. Because the present invention provides a plurality of amplification products from any given primer pair (depending on the bioagent being analyzed), multiple amplification products from different specific nucleic acid sequences may be obtained. Thus, the term “target” is not used to refer to a single specific nucleic acid sequence. The “target” is sought to be sorted out from other nucleic acid sequences and contains a sequence that has at least partial complementarity with an oligonucleotide primer. The target nucleic acid may comprise single- or double-stranded DNA or RNA. A “segment” is defined as a region of nucleic acid within the target sequence.

The term “template” refers to a strand of nucleic acid on which a complementary copy is built from nucleoside triphosphates through the activity of a template-dependent nucleic acid polymerase. Within a duplex the template strand is, by convention, depicted and described as the “bottom” strand. Similarly, the non-template strand is often depicted and described as the “top” strand.

As used herein, the term “T_(m)” is used in reference to the “melting temperature.” The melting temperature is the temperature at which a population of double-stranded nucleic acid molecules becomes half dissociated into single strands. Several equations for calculating the T_(m) of nucleic acids are well known in the art. As indicated by standard references, a simple estimate of the T_(m) value may be calculated by the equation: T_(m)=81.5+0.41(% G+C), when a nucleic acid is in aqueous solution at 1 M NaCl (see e.g., Anderson and Young, Quantitative Filter Hybridization, in Nucleic Acid Hybridization (1985). Other references (e.g., Allawi, H. T. & SantaLucia, J., Jr. Thermodynamics and NMR of internal G. T mismatches in DNA. Biochemistry 36, 10581-94 (1997) include more sophisticated computations which take structural and environmental, as well as sequence characteristics into account for the calculation of T_(m).

The term “triangulation genotyping analysis” refers to a method of genotyping a bioagent by measurement of molecular masses or base compositions of amplification products, corresponding to bioagent identifying amplicons, obtained by amplification of regions of more than one gene. In this sense, the term “triangulation” refers to a method of establishing the accuracy of information by comparing three or more types of independent points of view bearing on the same findings. Triangulation genotyping analysis carried out with a plurality of triangulation genotyping analysis primers yields a plurality of base compositions that then provide a pattern or “barcode” from which a species type can be assigned. The species type may represent a previously known sub-species or strain, or may be a previously unknown strain having a specific and previously unobserved base composition barcode indicating the existence of a previously unknown genotype.

As used herein, the term “triangulation genotyping analysis primer pair” is a primer pair designed to produce bioagent identifying amplicons for determining species types in a triangulation genotyping analysis.

The employment of more than one bioagent identifying amplicon for identification of a bioagent is herein referred to as “triangulation identification.” Triangulation identification is pursued by analyzing a plurality of bioagent identifying amplicons produced with different primer pairs. This process is used to reduce false negative and false positive signals, and enable reconstruction of the origin of hybrid or otherwise engineered bioagents. For example, identification of the three part toxin genes typical of B. anthracis (Bowen et al., J. Appl. Microbiol., 1999, 87, 270-278) in the absence of the expected signatures from the B. anthracis genome would suggest a genetic engineering event.

In the context of this invention, the term “unknown bioagent” may mean either: (i) a bioagent whose existence is known (such as the well known bacterial species Staphylococcus aureus for example) but which is not known to be in a sample to be analyzed, or (ii) a bioagent whose existence is not known (for example, the SARS coronavirus was unknown prior to April 2003). For example, if the method for identification of coronaviruses disclosed in commonly owned U.S. patent Ser. No. 10/829,826 (incorporated herein by reference in its entirety) was to be employed prior to April 2003 to identify the SARS coronavirus in a clinical sample, both meanings of “unknown” bioagent are applicable since the SARS coronavirus was unknown to science prior to April, 2003 and since it was not known what bioagent (in this case a coronavirus) was present in the sample. On the other hand, if the method of U.S. patent Ser. No. 10/829,826 was to be employed subsequent to April 2003 to identify the SARS coronavirus in a clinical sample, only the first meaning (i) of “unknown” bioagent would apply since the SARS coronavirus became known to science subsequent to April 2003 and since it was not known what bioagent was present in the sample.

The term “variable sequence” as used herein refers to differences in nucleic acid sequence between two nucleic acids. For example, the genes of two different bacterial species may vary in sequence by the presence of single base substitutions and/or deletions or insertions of one or more nucleotides. These two forms of the structural gene are said to vary in sequence from one another. In the context of the present invention, “viral nucleic acid” includes, but is not limited to, DNA, RNA, or DNA that has been obtained from viral RNA, such as, for example, by performing a reverse transcription reaction. Viral RNA can either be single-stranded (of positive or negative polarity) or double-stranded.

The term “virus” refers to obligate, ultramicroscopic, parasites that are incapable of autonomous replication (i.e., replication requires the use of the host cell's machinery). Viruses can survive outside of a host cell but cannot replicate.

The term “wild-type” refers to a gene or a gene product that has the characteristics of that gene or gene product when isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designated the “normal” or “wild-type” form of the gene. In contrast, the term “modified”, “mutant” or “polymorphic” refers to a gene or gene product that displays modifications in sequence and or functional properties (i.e., altered characteristics) when compared to the wild-type gene or gene product. It is noted that naturally-occurring mutants can be isolated; these are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.

As used herein, a “wobble base” is a variation in a codon found at the third nucleotide position of a DNA triplet. Variations in conserved regions of sequence are often found at the third nucleotide position due to redundancy in the amino acid code.

DETAILED DESCRIPTION OF EMBODIMENTS

A. Bioagent Identifying Amplicons

The present invention provides methods for detection and identification of unknown bioagents using bioagent identifying amplicons. Primers are selected to hybridize to conserved sequence regions of nucleic acids derived from a bioagent, and which bracket variable sequence regions to yield a bioagent identifying amplicon, which can be amplified and which is amenable to molecular mass determination. The molecular mass then provides a means to uniquely identify the bioagent without a requirement for prior knowledge of the possible identity of the bioagent. The molecular mass or corresponding base composition signature of the amplification product is then matched against a database of molecular masses or base composition signatures. A match is obtained when an experimentally-determined molecular mass or base composition of an analyzed amplification product is compared with known molecular masses or base compositions of known bioagent identifying amplicons and the experimentally determined molecular mass or base composition is the same as the molecular mass or base composition of one of the known bioagent identifying amplicons. Alternatively, the experimentally-determined molecular mass or base composition may be within experimental error of the molecular mass or base composition of a known bioagent identifying amplicon and still be classified as a match. In some cases, the match may also be classified using a probability of match model such as the models described in U.S. Ser. No. 11/073,362, which is commonly owned and incorporated herein by reference in entirety. Furthermore, the method can be applied to rapid parallel multiplex analyses, the results of which can be employed in a triangulation identification strategy. The present method provides rapid throughput and does not require nucleic acid sequencing of the amplified target sequence for bioagent detection and identification.

Despite enormous biological diversity, all forms of life on earth share sets of essential, common features in their genomes. Since genetic data provide the underlying basis for identification of bioagents by the methods of the present invention, it is necessary to select segments of nucleic acids which ideally provide enough variability to distinguish each individual bioagent and whose molecular mass is amenable to molecular mass determination.

Unlike bacterial genomes, which exhibit conservation of numerous genes (i.e. housekeeping genes) across all organisms, viruses do not share a gene that is essential and conserved among all virus families. Therefore, viral identification is achieved within smaller groups of related viruses, such as members of a particular virus family or genus. For example, RNA-dependent RNA polymerase is present in all single-stranded RNA viruses and can be used for broad priming as well as resolution within the virus family.

In some embodiments of the present invention, at least one bacterial nucleic acid segment is amplified in the process of identifying the bacterial bioagent. Thus, the nucleic acid segments that can be amplified by the primers disclosed herein and that provide enough variability to distinguish each individual bioagent and whose molecular masses are amenable to molecular mass determination are herein described as bioagent identifying amplicons.

In some embodiments of the present invention, bioagent identifying amplicons comprise from about 45 to about 150 nucleobases (i.e. from about 45 to about 200 linked nucleosides), although both longer and short regions may be used. One of ordinary skill in the art will appreciate that the invention embodies compounds of 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, and 150 nucleobases in length, or any range therewithin.

It is the combination of the portions of the bioagent nucleic acid segment to which the primers hybridize (hybridization sites) and the variable region between the primer hybridization sites that comprises the bioagent identifying amplicon. Thus, it can be said that a given bioagent identifying amplicon is “defined by” a given pair of primers.

In some embodiments, bioagent identifying amplicons amenable to molecular mass determination which are produced by the primers described herein are either of a length, size or mass compatible with the particular mode of molecular mass determination or compatible with a means of providing a predictable fragmentation pattern in order to obtain predictable fragments of a length compatible with the particular mode of molecular mass determination. Such means of providing a predictable fragmentation pattern of an amplification product include, but are not limited to, cleavage with chemical reagents, restriction enzymes or cleavage primers, for example. Thus, in some embodiments, bioagent identifying amplicons are larger than 150 nucleobases and are amenable to molecular mass determination following restriction digestion. Methods of using restriction enzymes and cleavage primers are well known to those with ordinary skill in the art.

In some embodiments, amplification products corresponding to bioagent identifying amplicons are obtained using the polymerase chain reaction (PCR) that is a routine method to those with ordinary skill in the molecular biology arts. Other amplification methods may be used such as ligase chain reaction (LCR), low-stringency single primer PCR, and multiple strand displacement amplification (MDA). These methods are also known to those with ordinary skill.

B. Primers and Primer Pairs

In some embodiments, the primers are designed to bind to conserved sequence regions of a bioagent identifying amplicon that flank an intervening variable region and yield amplification products which provide variability sufficient to distinguish each individual bioagent, and which are amenable to molecular mass analysis. In some embodiments, the highly conserved sequence regions exhibit between about 80-100%, or between about 90-100%, or between about 95-100% identity, or between about 99-100% identity. The molecular mass of a given amplification product provides a means of identifying the bioagent from which it was obtained, due to the variability of the variable region. Thus, design of the primers involves selection of a variable region with sufficient variability to resolve the identity of a given bioagent. In some embodiments, bioagent identifying amplicons are specific to the identity of the bioagent.

In some embodiments, identification of bioagents is accomplished at different levels using primers suited to resolution of each individual level of identification. Broad range survey primers are designed with the objective of identifying a bioagent as a member of a particular division (e.g., an order, family, genus or other such grouping of bioagents above the species level of bioagents). In some embodiments, broad range survey intelligent primers are capable of identification of bioagents at the species or sub-species level. Examples of broad range survey primers include, but are not limited to: primer pair numbers: 346 (SEQ ID NOs: 202:1110), 347 (SEQ ID NOs: 560:1278), 348 SEQ ID NOs: 706:895), and 361 (SEQ ID NOs: 697:1398) which target DNA encoding 16S rRNA, and primer pair numbers 349 (SEQ ID NOs: 401:1156) and 360 (SEQ ID NOs: 409:1434) which target DNA encoding 23S rRNA.

In some embodiments, drill-down primers are designed with the objective of identifying a bioagent at the sub-species level (including strains, subtypes, variants and isolates) based on sub-species characteristics which may, for example, include single nucleotide polymorphisms (SNPs), variable number tandem repeats (VNTRs), deletions, drug resistance mutations or any other modification of a nucleic acid sequence of a bioagent relative to other members of a species having different sub-species characteristics. Drill-down intelligent primers are not always required for identification at the sub-species level because broad range survey intelligent primers may, in some cases provide sufficient identification resolution to accomplishing this identification objective. Examples of drill-down primers include, but are not limited to: confirmation primer pairs such as primer pair numbers 351 (SEQ ID NOs: 355:1423) and 353 (SEQ ID NOs: 220:1394), which target the pX01 virulence plasmid of Bacillus anthracis. Other examples of drill-down primer pairs are found in sets of triangulation genotyping primer pairs such as, for example, the primer pair number 2146 (SEQ ID NOs: 437:1137) which targets the arcC gene (encoding carmabate kinase) and is included in an 8 primer pair panel or kit for use in genotyping Staphylococcus aureus, or in other panels or kits of primer pairs used for determining drug-resistant bacterial strains, such as, for example, primer pair number 2095 (SEQ ID NOs: 456:1261) which targets the pv-luk gene (encoding Panton-Valentine leukocidin) and is included in an 8 primer pair panel or kit for use in identification of drug resistant strains of Staphylococcus aureus.

A representative process flow diagram used for primer selection and validation process is outlined in FIG. 1. For each group of organisms, candidate target sequences are identified (200) from which nucleotide alignments are created (210) and analyzed (220). Primers are then designed by selecting appropriate priming regions (230) to facilitate the selection of candidate primer pairs (240). The primer pairs are then subjected to in silico analysis by electronic PCR (ePCR) (300) wherein bioagent identifying amplicons are obtained from sequence databases such as GenBank or other sequence collections (310) and checked for specificity in silico (320). Bioagent identifying amplicons obtained from GenBank sequences (310) can also be analyzed by a probability model which predicts the capability of a given amplicon to identify unknown bioagents such that the base compositions of amplicons with favorable probability scores are then stored in a base composition database (325). Alternatively, base compositions of the bioagent identifying amplicons obtained from the primers and GenBank sequences can be directly entered into the base composition database (330). Candidate primer pairs (240) are validated by testing their ability to hybridize to target nucleic acid by an in vitro amplification by a method such as PCR analysis (400) of nucleic acid from a collection of organisms (410). Amplification products thus obtained are analyzed by gel electrophoresis or by mass spectrometry to confirm the sensitivity, specificity and reproducibility of the primers used to obtain the amplification products (420).

Many of the important pathogens, including the organisms of greatest concern as biowarfare agents, have been completely sequenced. This effort has greatly facilitated the design of primers for the detection of unknown bioagents. The combination of broad-range priming with division-wide and drill-down priming has been used very successfully in several applications of the technology, including environmental surveillance for biowarfare threat agents and clinical sample analysis for medically important pathogens.

Synthesis of primers is well known and routine in the art. The primers may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed.

In some embodiments primers are employed as compositions for use in methods for identification of bacterial bioagents as follows: a primer pair composition is contacted with nucleic acid (such as, for example, bacterial DNA or DNA reverse transcribed from the rRNA) of an unknown bacterial bioagent. The nucleic acid is then amplified by a nucleic acid amplification technique, such as PCR for example, to obtain an amplification product that represents a bioagent identifying amplicon. The molecular mass of each strand of the double-stranded amplification product is determined by a molecular mass measurement technique such as mass spectrometry for example, wherein the two strands of the double-stranded amplification product are separated during the ionization process. In some embodiments, the mass spectrometry is electrospray Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) or electrospray time of flight mass spectrometry (ESI-TOF-MS). A list of possible base compositions can be generated for the molecular mass value obtained for each strand and the choice of the correct base composition from the list is facilitated by matching the base composition of one strand with a complementary base composition of the other strand. The molecular mass or base composition thus determined is then compared with a database of molecular masses or base compositions of analogous bioagent identifying amplicons for known viral bioagents. A match between the molecular mass or base composition of the amplification product and the molecular mass or base composition of an analogous bioagent identifying amplicon for a known viral bioagent indicates the identity of the unknown bioagent. In some embodiments, the primer pair used is one of the primer pairs of Table 2. In some embodiments, the method is repeated using one or more different primer pairs to resolve possible ambiguities in the identification process or to improve the confidence level for the identification assignment.

In some embodiments, a bioagent identifying amplicon may be produced using only a single primer (either the forward or reverse primer of any given primer pair), provided an appropriate amplification method is chosen, such as, for example, low stringency single primer PCR (LSSP-PCR). Adaptation of this amplification method in order to produce bioagent identifying amplicons can be accomplished by one with ordinary skill in the art without undue experimentation.

In some embodiments, the oligonucleotide primers are broad range survey primers which hybridize to conserved regions of nucleic acid encoding the hexon gene of all (or between 80% and 100%, between 85% and 100%, between 90% and 100% or between 95% and 100%) known bacteria and produce bacterial bioagent identifying amplicons.

In some cases, the molecular mass or base composition of a bacterial bioagent identifying amplicon defined by a broad range survey primer pair does not provide enough resolution to unambiguously identify a bacterial bioagent at or below the species level. These cases benefit from further analysis of one or more bacterial bioagent identifying amplicons generated from at least one additional broad range survey primer pair or from at least one additional division-wide primer pair. The employment of more than one bioagent identifying amplicon for identification of a bioagent is herein referred to as triangulation identification.

In other embodiments, the oligonucleotide primers are division-wide primers which hybridize to nucleic acid encoding genes of species within a genus of bacteria. In other embodiments, the oligonucleotide primers are drill-down primers which enable the identification of sub-species characteristics. Drill down primers provide the functionality of producing bioagent identifying amplicons for drill-down analyses such as strain typing when contacted with nucleic acid under amplification conditions. Identification of such sub-species characteristics is often critical for determining proper clinical treatment of viral infections. In some embodiments, sub-species characteristics are identified using only broad range survey primers and division-wide and drill-down primers are not used.

In some embodiments, the primers used for amplification hybridize to and amplify genomic DNA, and DNA of bacterial plasmids.

In some embodiments, various computer software programs may be used to aid in design of primers for amplification reactions such as Primer Premier 5 (Premier Biosoft, Palo Alto, Calif,) or OLIGO Primer Analysis Software (Molecular Biology Insights, Cascade, Colo.). These programs allow the user to input desired hybridization conditions such as melting temperature of a primer-template duplex for example. In some embodiments, an in silico PCR search algorithm, such as (ePCR) is used to analyze primer specificity across a plurality of template sequences which can be readily obtained from public sequence databases such as GenBank for example. An existing RNA structure search algorithm (Macke et al., Nucl. Acids Res., 2001, 29, 4724-4735, which is incorporated herein by reference in its entirety) has been modified to include PCR parameters such as hybridization conditions, mismatches, and thermodynamic calculations (SantaLucia, Proc. Natl. Acad. Sci. U.S.A., 1998, 95, 1460-1465, which is incorporated herein by reference in its entirety). This also provides information on primer specificity of the selected primer pairs. In some embodiments, the hybridization conditions applied to the algorithm can limit the results of primer specificity obtained from the algorithm. In some embodiments, the melting temperature threshold for the primer template duplex is specified to be 35° C. or a higher temperature. In some embodiments the number of acceptable mismatches is specified to be seven mismatches or less. In some embodiments, the buffer components and concentrations and primer concentrations may be specified and incorporated into the algorithm, for example, an appropriate primer concentration is about 250 nM and appropriate buffer components are 50 mM sodium or potassium and 1.5 mM Mg²⁺.

One with ordinary skill in the art of design of amplification primers will recognize that a given primer need not hybridize with 100% complementarity in order to effectively prime the synthesis of a complementary nucleic acid strand in an amplification reaction. Moreover, a primer may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event. (e.g., for example, a loop structure or a hairpin structure). The primers of the present invention may comprise at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% sequence identity with any of the primers listed in Table 2. Thus, in some embodiments of the present invention, an extent of variation of 70% to 100%, or any range therewithin, of the sequence identity is possible relative to the specific primer sequences disclosed herein. Determination of sequence identity is described in the following example: a primer 20 nucleobases in length which is identical to another 20 nucleobase primer having two non-identical residues has 18 of 20 identical residues (18/20=0.9 or 90% sequence identity). In another example, a primer 15 nucleobases in length having all residues identical to a 15 nucleobase segment of primer 20 nucleobases in length would have 15/20=0.75 or 75% sequence identity with the 20 nucleobase primer.

Percent homology, sequence identity or complementarity, can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for UNIX, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489). In some embodiments, complementarity of primers with respect to the conserved priming regions of viral nucleic acid is between about 70% and about 75% 80%. In other embodiments, homology, sequence identity or complementarity, is between about 75% and about 80%. In yet other embodiments, homology, sequence identity or complementarity, is at least 85%, at least 90%, at least 92%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or is 100%.

In some embodiments, the primers described herein comprise at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 92%, at least 94%, at least 95%, at least 96%, at least 98%, or at least 99%, or 100% (or any range therewithin) sequence identity with the primer sequences specifically disclosed herein.

One with ordinary skill is able to calculate percent sequence identity or percent sequence homology and able to determine, without undue experimentation, the effects of variation of primer sequence identity on the function of the primer in its role in priming synthesis of a complementary strand of nucleic acid for production of an amplification product of a corresponding bioagent identifying amplicon.

In one embodiment, the primers are at least 13 nucleobases in length. In another embodiment, the primers are less than 36 nucleobases in length.

In some embodiments of the present invention, the oligonucleotide primers are 13 to 35 nucleobases in length (13 to 35 linked nucleotide residues). These embodiments comprise oligonucleotide primers 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 nucleobases in length, or any range therewithin. The present invention contemplates using both longer and shorter primers. Furthermore, the primers may also be linked to one or more other desired moieties, including, but not limited to, affinity groups, ligands, regions of nucleic acid that are not complementary to the nucleic acid to be amplified, labels, etc. Primers may also form hairpin structures. For example, hairpin primers may be used to amplify short target nucleic acid molecules. The presence of the hairpin may stabilize the amplification complex (see e.g., TAQMAN MicroRNA Assays, Applied Biosystems, Foster City, Calif.).

In some embodiments, any oligonucleotide primer pair may have one or both primers with less then 70% sequence homology with a corresponding member of any of the primer pairs of Table 2 if the primer pair has the capability of producing an amplification product corresponding to a bioagent identifying amplicon. In other embodiments, any oligonucleotide primer pair may have one or both primers with a length greater than 35 nucleobases if the primer pair has the capability of producing an amplification product corresponding to a bioagent identifying amplicon.

In some embodiments, the function of a given primer may be substituted by a combination of two or more primers segments that hybridize adjacent to each other or that are linked by a nucleic acid loop structure or linker which allows a polymerase to extend the two or more primers in an amplification reaction.

In some embodiments, the primer pairs used for obtaining bioagent identifying amplicons are the primer pairs of Table 2. In other embodiments, other combinations of primer pairs are possible by combining certain members of the forward primers with certain members of the reverse primers. An example can be seen in Table 2 for two primer pair combinations of forward primer 16S_EC_(—)789_(—)810F (SEQ ID NO:206), with the reverse primers 16S_EC_(—)880_(—)894_R (SEQ ID NO: 796), or 16 S_EC_(—)882_(—)899_R or (SEQ ID NO: 818). Arriving at a favorable alternate size of the bioagent identifying amplicon that would be produced by the primer pair, which preferably is between about 45 to about 150 nucleobases in length. Alternatively, a bioagent identifying amplicon longer than 150 nucleobases in length could be cleaved into smaller segments by cleavage reagents such as chemical reagents, or restriction enzymes, for example.

In some embodiments, the primers are configured to amplify nucleic acid of a bioagent to produce amplification products that can be measured by mass spectrometry and from whose molecular masses candidate base compositions can be readily calculated.

In some embodiments, any given primer comprises a modification comprising the addition of a non-templated T residue to the 5′ end of the primer (i.e., the added T residue does not necessarily hybridize to the nucleic acid being amplified). The addition of a non-templated T residue has an effect of minimizing the addition of non-templated adenosine residues as a result of the non-specific enzyme activity of Taq polymerase (Magnuson et al., Biotechniques, 1996, 21, 700-709), an occurrence which may lead to ambiguous results arising from molecular mass analysis.

In some embodiments of the present invention, primers may contain one or more universal bases. Because any variation (due to codon wobble in the 3^(rd) position) in the conserved regions among species is likely to occur in the third position of a DNA (or RNA) triplet, oligonucleotide primers can be designed such that the nucleotide corresponding to this position is a base which can bind to more than one nucleotide, referred to herein as a “universal nucleobase.” For example, under this “wobble” pairing, inosine (I) binds to U, C or A; guanine (G) binds to U or C, and uridine (U) binds to U or C. Other examples of universal nucleobases include nitroindoles such as 5-nitroindole or 3-nitropyrrole (Loakes et al., Nucleosides and Nucleotides, 1995, 14, 1001-1003), the degenerate nucleotides dP or dK (Hill et al.), an acyclic nucleoside analog containing 5-nitroindazole (Van Aerschot et al., Nucleosides and Nucleotides, 1995, 14, 1053-1056) or the purine analog 1-(2-deoxy-p-D-ribofuranosyl)-imidazole-4-carboxamide (Sala et al., Nucl. Acids Res., 1996, 24, 3302-3306).

In some embodiments, to compensate for the somewhat weaker binding by the wobble base, the oligonucleotide primers are designed such that the first and second positions of each triplet are occupied by nucleotide analogs that bind with greater affinity than the unmodified nucleotide. Examples of these analogs include, but are not limited to, 2,6-diaminopurine which binds to thymine, 5-propynyluracil (also known as propynylated thymine) which binds to adenine and 5-propynylcytosine and phenoxazines, including G-clamp, which binds to G. Propynylated pyrimidines are described in U.S. Pat. Nos. 5,645,985, 5,830,653 and 5,484,908, each of which is commonly owned and incorporated herein by reference in its entirety. Propynylated primers are described in U.S Pre-Grant Publication No. 2003-0170682, which is also commonly owned and incorporated herein by reference in its entirety. Phenoxazines are described in U.S. Pat. Nos. 5,502,177, 5,763,588, and 6,005,096, each of which is incorporated herein by reference in its entirety. G-clamps are described in U.S. Pat. Nos. 6,007,992 and 6,028,183, each of which is incorporated herein by reference in its entirety.

In some embodiments, primer hybridization is enhanced using primers containing 5-propynyl deoxy-cytidine and deoxy-thymidine nucleotides. These modified primers offer increased affinity and base pairing selectivity.

In some embodiments, non-template primer tags are used to increase the melting temperature (T_(m)) of a primer-template duplex in order to improve amplification efficiency. A non-template tag is at least three consecutive A or T nucleotide residues on a primer which are not complementary to the template. In any given non-template tag, A can be replaced by C or G and T can also be replaced by C or G. Although Watson-Crick hybridization is not expected to occur for a non-template tag relative to the template, the extra hydrogen bond in a G-C pair relative to an A-T pair confers increased stability of the primer-template duplex and improves amplification efficiency for subsequent cycles of amplification when the primers hybridize to strands synthesized in previous cycles.

In other embodiments, propynylated tags may be used in a manner similar to that of the non-template tag, wherein two or more 5-propynylcytidine or 5-propynyluridine residues replace template matching residues on a primer. In other embodiments, a primer contains a modified internucleoside linkage such as a phosphorothioate linkage, for example.

In some embodiments, the primers contain mass-modifying tags. Reducing the total number of possible base compositions of a nucleic acid of specific molecular weight provides a means of avoiding a persistent source of ambiguity in determination of base composition of amplification products. Addition of mass-modifying tags to certain nucleobases of a given primer will result in simplification of de novo determination of base composition of a given bioagent identifying amplicon from its molecular mass.

In some embodiments of the present invention, the mass modified nucleobase comprises one or more of the following: for example, 7-deaza-2′-deoxyadenosine-5-triphosphate, 5-iodo-2′-deoxyuridine-5′-triphosphate, 5-bromo-2′-deoxyuridine-5′-triphosphate, 5-bromo-2′-deoxycytidine-5′-triphosphate, 5-iodo-2′-deoxycytidine-5′-triphosphate, 5-hydroxy-2′-deoxyuridine-5′-triphosphate, 4-thiothymidine-5′-triphosphate, 5-aza-2′-deoxyuridine-5′-triphosphate, 5-fluoro-2′-deoxyuridine-5′-triphosphate, O6-methyl-2′-deoxyguanosine-5′-triphosphate, N2-methyl-2′-deoxyguanosine-5′-triphosphate, 8-oxo-2′-deoxyguanosine-5′-triphosphate or thiothymidine-5′-triphosphate. In some embodiments, the mass-modified nucleobase comprises ¹⁵N or ¹³C or both ¹⁵N and ¹³C.

In some embodiments, multiplex amplification is performed where multiple bioagent identifying amplicons are amplified with a plurality of primer pairs. The advantages of multiplexing are that fewer reaction containers (for example, wells of a 96- or 384-well plate) are needed for each molecular mass measurement, providing time, resource and cost savings because additional bioagent identification data can be obtained within a single analysis. Multiplex amplification methods are well known to those with ordinary skill and can be developed without undue experimentation. However, in some embodiments, one useful and non-obvious step in selecting a plurality candidate bioagent identifying amplicons for multiplex amplification is to ensure that each strand of each amplification product will be sufficiently different in molecular mass that mass spectral signals will not overlap and lead to ambiguous analysis results. In some embodiments, a 10 Da difference in mass of two strands of one or more amplification products is sufficient to avoid overlap of mass spectral peaks.

In some embodiments, as an alternative to multiplex amplification, single amplification reactions can be pooled before analysis by mass spectrometry. In these embodiments, as for multiplex amplification embodiments, it is useful to select a plurality of candidate bioagent identifying amplicons to ensure that each strand of each amplification product will be sufficiently different in molecular mass that mass spectral signals will not overlap and lead to ambiguous analysis results.

C Determination of Molecular Mass of Bioagent Identifying Amplicons

In some embodiments, the molecular mass of a given bioagent identifying amplicon is determined by mass spectrometry. Mass spectrometry has several advantages, not the least of which is high bandwidth characterized by the ability to separate (and isolate) many molecular peaks across a broad range of mass to charge ratio (m/z). Thus mass spectrometry is intrinsically a parallel detection scheme without the need for radioactive or fluorescent labels, since every amplification product is identified by its molecular mass. The current state of the art in mass spectrometry is such that less than femtomole quantities of material can be readily analyzed to afford information about the molecular contents of the sample. An accurate assessment of the molecular mass of the material can be quickly obtained, irrespective of whether the molecular weight of the sample is several hundred, or in excess of one hundred thousand atomic mass units (amu) or Daltons.

In some embodiments, intact molecular ions are generated from amplification products using one of a variety of ionization techniques to convert the sample to gas phase. These ionization methods include, but are not limited to, electrospray ionization (ES), matrix-assisted laser desorption ionization (MALDI) and fast atom bombardment (FAB). Upon ionization, several peaks are observed from one sample due to the formation of ions with different charges. Averaging the multiple readings of molecular mass obtained from a single mass spectrum affords an estimate of molecular mass of the bioagent identifying amplicon. Electrospray ionization mass spectrometry (ESI-MS) is particularly useful for very high molecular weight polymers such as proteins and nucleic acids having molecular weights greater than 10 kDa, since it yields a distribution of multiply-charged molecules of the sample without causing a significant amount of fragmentation.

The mass detectors used in the methods of the present invention include, but are not limited to, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), time of flight (TOF), ion trap, quadrupole, magnetic sector, Q-TOF, and triple quadrupole.

D. Base Compositions of Bioagent Identifying Amplicons

Although the molecular mass of amplification products obtained using intelligent primers provides a means for identification of bioagents, conversion of molecular mass data to a base composition signature is useful for certain analyses. As used herein, “base composition” is the exact number of each nucleobase (A, T, C and G) determined from the molecular mass of a bioagent identifying amplicon. In some embodiments, a base composition provides an index of a specific organism. Base compositions can be calculated from known sequences of known bioagent identifying amplicons and can be experimentally determined by measuring the molecular mass of a given bioagent identifying amplicon, followed by determination of all possible base compositions which are consistent with the measured molecular mass within acceptable experimental error. The following example illustrates determination of base composition from an experimentally obtained molecular mass of a 46-mer amplification product originating at position 1337 of the 16S rRNA of Bacillus anthracis. The forward and reverse strands of the amplification product have measured molecular masses of 14208 and 14079 Da, respectively. The possible base compositions derived from the molecular masses of the forward and reverse strands for the B. anthracis products are listed in Table 1. TABLE 1 Possible Base Compositions for B. anthracis 46mer Amplification Product Calc. Mass Mass Error Base Calc. Mass Mass Error Base Forward Forward Composition of Reverse Reverse Composition of Strand Strand Forward Strand Strand Strand Reverse Strand 14208.2935 0.079520 A1 G17 C10 T18 14079.2624 0.080600 A0 G14 C13 T19 14208.3160 0.056980 A1 G20 C15 T10 14079.2849 0.058060 A0 G17 C18 T11 14208.3386 0.034440 A1 G23 C20 T2 14079.3075 0.035520 A0 G20 C23 T3 14208.3074 0.065560 A6 G11 C3 T26 14079.2538 0.089180 A5 G5 C1 T35 14208.3300 0.043020 A6 G14 C8 T18 14079.2764 0.066640 A5 G8 C6 T27 14208.3525 0.020480 A6 G17 C13 T10 14079.2989 0.044100 A5 G11 C11 T19 14208.3751 0.002060 A6 G20 C18 T2 14079.3214 0.021560 A5 G14 C16 T11 14208.3439 0.029060 A11 G8 C1 T26 14079.3440 0.000980 A5 G17 C21 T3 14208.3665 0.006520 A11 G11 C6 T18 14079.3129 0.030140 A10 G5 C4 T27 14208.3890 0.016020 A11 G14 C11 T10 14079.3354 0.007600 A10 G8 C9 T19 14208.4116 0.038560 A11 G17 C16 T2 14079.3579 0.014940 A10 G11 C14 T11 14208.4030 0.029980 A16 G8 C4 T18 14079.3805 0.037480 A10 G14 C19 T3 14208.4255 0.052520 A16 G11 C9 T10 14079.3494 0.006360 A15 G2 C2 T27 14208.4481 0.075060 A16 G14 C14 T2 14079.3719 0.028900 A15 G5 C7 T19 14208.4395 0.066480 A21 G5 C2 T18 14079.3944 0.051440 A15 G8 C12 T11 14208.4620 0.089020 A21 G8 C7 T10 14079.4170 0.073980 A15 G11 C17 T3 — — — 14079.4084 0.065400 A20 G2 C5 T19 — — — 14079.4309 0.087940 A20 G5 C10 T13

Among the 16 possible base compositions for the forward strand and the 18 possible base compositions for the reverse strand that were calculated, only one pair (shown in bold) are complementary base compositions, which indicates the true base composition of the amplification product. It should be recognized that this logic is applicable for determination of base compositions of any bioagent identifying amplicon, regardless of the class of bioagent from which the corresponding amplification product was obtained.

In some embodiments, assignment of previously unobserved base compositions (also known as “true unknown base compositions”) to a given phylogeny can be accomplished via the use of pattern classifier model algorithms. Base compositions, like sequences, vary slightly from strain to strain within species, for example. In some embodiments, the pattern classifier model is the mutational probability model. On other embodiments, the pattern classifier is the polytope model. The mutational probability model and polytope model are both commonly owned and described in U.S. patent application Ser. No. 11/073,362 which is incorporated herein by reference in entirety.

In one embodiment, it is possible to manage this diversity by building “base composition probability clouds” around the composition constraints for each species. This permits identification of organisms in a fashion similar to sequence analysis. A “pseudo four-dimensional plot” can be used to visualize the concept of base composition probability clouds. Optimal primer design requires optimal choice of bioagent identifying amplicons and maximizes the separation between the base composition signatures of individual bioagents. Areas where clouds overlap indicate regions that may result in a misclassification, a problem which is overcome by a triangulation identification process using bioagent identifying amplicons not affected by overlap of base composition probability clouds.

In some embodiments, base composition probability clouds provide the means for screening potential primer pairs in order to avoid potential misclassifications of base compositions. In other embodiments, base composition probability clouds provide the means for predicting the identity of a bioagent whose assigned base composition was not previously observed and/or indexed in a bioagent identifying amplicon base composition database due to evolutionary transitions in its nucleic acid sequence. Thus, in contrast to probe-based techniques, mass spectrometry determination of base composition does not require prior knowledge of the composition or sequence in order to make the measurement.

The present invention provides bioagent classifying information similar to DNA sequencing and phylogenetic analysis at a level sufficient to identify a given bioagent. Furthermore, the process of determination of a previously unknown base composition for a given bioagent (for example, in a case where sequence information is unavailable) has downstream utility by providing additional bioagent indexing information with which to populate base composition databases. The process of future bioagent identification is thus greatly improved as more BCS indexes become available in base composition databases.

E. Triangulation Identification

In some cases, a molecular mass of a single bioagent identifying amplicon alone does not provide enough resolution to unambiguously identify a given bioagent. The employment of more than one bioagent identifying amplicon for identification of a bioagent is herein referred to as “triangulation identification.” Triangulation identification is pursued by determining the molecular masses of a plurality of bioagent identifying amplicons selected within a plurality of housekeeping genes. This process is used to reduce false negative and false positive signals, and enable reconstruction of the origin of hybrid or otherwise engineered bioagents. For example, identification of the three part toxin genes typical of B. anthracis (Bowen et al., J. Appl. Microbiol., 1999, 87, 270-278) in the absence of the expected signatures from the B. anthracis genome would suggest a genetic engineering event.

In some embodiments, the triangulation identification process can be pursued by characterization of bioagent identifying amplicons in a massively parallel fashion using the polymerase chain reaction (PCR), such as multiplex PCR where multiple primers are employed in the same amplification reaction mixture, or PCR in multi-well plate format wherein a different and unique pair of primers is used in multiple wells containing otherwise identical reaction mixtures. Such multiplex and multi-well PCR methods are well known to those with ordinary skill in the arts of rapid throughput amplification of nucleic acids. In other related embodiments, one PCR reaction per well or container may be carried out, followed by an amplicon pooling step wherein the amplification products of different wells are combined in a single well or container which is then subjected to molecular mass analysis. The combination of pooled amplicons can be chosen such that the expected ranges of molecular masses of individual amplicons are not overlapping and thus will not complicate identification of signals.

F. Codon Base Composition Analysis

In some embodiments of the present invention, one or more nucleotide substitutions within a codon of a gene of an infectious organism confer drug resistance upon an organism which can be determined by codon base composition analysis. The organism can be a bacterium, virus, fungus or protozoan.

In some embodiments, the amplification product containing the codon being analyzed is of a length of about 35 to about 200 nucleobases. The primers employed in obtaining the amplification product can hybridize to upstream and downstream sequences directly adjacent to the codon, or can hybridize to upstream and downstream sequences one or more sequence positions away from the codon. The primers may have between about 70% to 100% sequence complementarity with the sequence of the gene containing the codon being analyzed.

In some embodiments, the codon base composition analysis is undertaken

In some embodiments, the codon analysis is undertaken for the purpose of investigating genetic disease in an individual. In other embodiments, the codon analysis is undertaken for the purpose of investigating a drug resistance mutation or any other deleterious mutation in an infectious organism such as a bacterium, virus, fungus or protozoan. In some embodiments, the bioagent is a bacterium identified in a biological product.

In some embodiments, the molecular mass of an amplification product containing the codon being analyzed is measured by mass spectrometry. The mass spectrometry can be either electrospray (ESI) mass spectrometry or matrix-assisted laser desorption ionization (MALDI) mass spectrometry. Time-of-flight (TOF) is an example of one mode of mass spectrometry compatible with the analyses of the present invention.

The methods of the present invention can also be employed to determine the relative abundance of drug resistant strains of the organism being analyzed. Relative abundances can be calculated from amplitudes of mass spectral signals with relation to internal calibrants. In some embodiments, known quantities of internal amplification calibrants can be included in the amplification reactions and abundances of analyte amplification product estimated in relation to the known quantities of the calibrants.

In some embodiments, upon identification of one or more drug-resistant strains of an infectious organism infecting an individual, one or more alternative treatments can be devised to treat the individual.

G. Determination of the Quantity of a Bioagent

In some embodiments, the identity and quantity of an unknown bioagent can be determined using the process illustrated in FIG. 2. Primers (500) and a known quantity of a calibration polynucleotide (505) are added to a sample containing nucleic acid of an unknown bioagent. The total nucleic acid in the sample is then subjected to an amplification reaction (510) to obtain amplification products. The molecular masses of amplification products are determined (515) from which are obtained molecular mass and abundance data. The molecular mass of the bioagent identifying amplicon (520) provides the means for its identification (525) and the molecular mass of the calibration amplicon obtained from the calibration polynucleotide (530) provides the means for its identification (535). The abundance data of the bioagent identifying amplicon is recorded (540) and the abundance data for the calibration data is recorded (545), both of which are used in a calculation (550) which determines the quantity of unknown bioagent in the sample.

A sample comprising an unknown bioagent is contacted with a pair of primers that provide the means for amplification of nucleic acid from the bioagent, and a known quantity of a polynucleotide that comprises a calibration sequence. The nucleic acids of the bioagent and of the calibration sequence are amplified and the rate of amplification is reasonably assumed to be similar for the nucleic acid of the bioagent and of the calibration sequence. The amplification reaction then produces two amplification products: a bioagent identifying amplicon and a calibration amplicon. The bioagent identifying amplicon and the calibration amplicon should be distinguishable by molecular mass while being amplified at essentially the same rate. Effecting differential molecular masses can be accomplished by choosing as a calibration sequence, a representative bioagent identifying amplicon (from a specific species of bioagent) and performing, for example, a 2-8 nucleobase deletion or insertion within the variable region between the two priming sites. The amplified sample containing the bioagent identifying amplicon and the calibration amplicon is then subjected to molecular mass analysis by mass spectrometry, for example. The resulting molecular mass analysis of the nucleic acid of the bioagent and of the calibration sequence provides molecular mass data and abundance data for the nucleic acid of the bioagent and of the calibration sequence. The molecular mass data obtained for the nucleic acid of the bioagent enables identification of the unknown bioagent and the abundance data enables calculation of the quantity of the bioagent, based on the knowledge of the quantity of calibration polynucleotide contacted with the sample.

In some embodiments, construction of a standard curve where the amount of calibration polynucleotide spiked into the sample is varied provides additional resolution and improved confidence for the determination of the quantity of bioagent in the sample. The use of standard curves for analytical determination of molecular quantities is well known to one with ordinary skill and can be performed without undue experimentation.

In some embodiments, multiplex amplification is performed where multiple bioagent identifying amplicons are amplified with multiple primer pairs which also amplify the corresponding standard calibration sequences. In this or other embodiments, the standard calibration sequences are optionally included within a single vector which functions as the calibration polynucleotide. Multiplex amplification methods are well known to those with ordinary skill and can be performed without undue experimentation.

In some embodiments, the calibrant polynucleotide is used as an internal positive control to confirm that amplification conditions and subsequent analysis steps are successful in producing a measurable amplicon. Even in the absence of copies of the genome of a bioagent, the calibration polynucleotide should give rise to a calibration amplicon. Failure to produce a measurable calibration amplicon indicates a failure of amplification or subsequent analysis step such as amplicon purification or molecular mass determination. Reaching a conclusion that such failures have occurred is in itself, a useful event.

In some embodiments, the calibration sequence is comprised of DNA. In some embodiments, the calibration sequence is comprised of RNA.

In some embodiments, the calibration sequence is inserted into a vector that itself functions as the calibration polynucleotide. In some embodiments, more than one calibration sequence is inserted into the vector that functions as the calibration polynucleotide. Such a calibration polynucleotide is herein termed a “combination calibration polynucleotide.” The process of inserting polynucleotides into vectors is routine to those skilled in the art and can be accomplished without undue experimentation. Thus, it should be recognized that the calibration method should not be limited to the embodiments described herein. The calibration method can be applied for determination of the quantity of any bioagent identifying amplicon when an appropriate standard calibrant polynucleotide sequence is designed and used. The process of choosing an appropriate vector for insertion of a calibrant is also a routine operation that can be accomplished by one with ordinary skill without undue experimentation.

H. Identification of Bacteria

In other embodiments of the present invention, the primer pairs produce bioagent identifying amplicons within stable and highly conserved regions of bacteria. The advantage to characterization of an amplicon defined by priming regions that fall within a highly conserved region is that there is a low probability that the region will evolve past the point of primer recognition, in which case, the primer hybridization of the amplification step would fail. Such a primer set is thus useful as a broad range survey-type primer. In another embodiment of the present invention, the intelligent primers produce bioagent identifying amplicons including a region which evolves more quickly than the stable region described above. The advantage of characterization bioagent identifying amplicon corresponding to an evolving genomic region is that it is useful for distinguishing emerging strain variants or the presence of virulence genes, drug resistance genes, or codon mutations that induce drug resistance.

The present invention also has significant advantages as a platform for identification of diseases caused by emerging bacterial strains such as, for example, drug-resistant strains of Staphylococcus aureus. The present invention eliminates the need for prior knowledge of bioagent sequence to generate hybridization probes. This is possible because the methods are not confounded by naturally occurring evolutionary variations occurring in the sequence acting as the template for production of the bioagent identifying amplicon. Measurement of molecular mass and determination of base composition is accomplished in an unbiased manner without sequence prejudice.

Another embodiment of the present invention also provides a means of tracking the spread of a bacterium, such as a particular drug-resistant strain when a plurality of samples obtained from different locations are analyzed by the methods described above in an epidemiological setting. In one embodiment, a plurality of samples from a plurality of different locations is analyzed with primer pairs which produce bioagent identifying amplicons, a subset of which contains a specific drug-resistant bacterial strain. The corresponding locations of the members of the drug-resistant strain subset indicate the spread of the specific drug-resistant strain to the corresponding locations.

I. Kits

The present invention also provides kits for carrying out the methods described herein. In some embodiments, the kit may comprise a sufficient quantity of one or more primer pairs to perform an amplification reaction on a target polynucleotide from a bioagent to form a bioagent identifying amplicon. In some embodiments, the kit may comprise from one to fifty primer pairs, from one to twenty primer pairs, from one to ten primer pairs, or from two to five primer pairs. In some embodiments, the kit may comprise one or more primer pairs recited in Table 2.

In some embodiments, the kit comprises one or more broad range survey primer(s), division wide primer(s), or drill-down primer(s), or any combination thereof. If a given problem involves identification of a specific bioagent, the solution to the problem may require the selection of a particular combination of primers to provide the solution to the problem. A kit may be designed so as to comprise particular primer pairs for identification of a particular bioagent. A drill-down kit may be used, for example, to distinguish different genotypes or strains, drug-resistant, or otherwise. In some embodiments, the primer pair components of any of these kits may be additionally combined to comprise additional combinations of broad range survey primers and division-wide primers so as to be able to identify a bacterium.

In some embodiments, the kit contains standardized calibration polynucleotides for use as internal amplification calibrants. Internal calibrants are described in commonly owned U.S. patent application Ser. No. 60/545,425 which is incorporated herein by reference in its entirety.

In some embodiments, the kit comprises a sufficient quantity of reverse transcriptase (if RNA is to be analyzed for example), a DNA polymerase, suitable nucleoside triphosphates (including alternative dNTPs such as inosine or modified dNTPs such as the 5-propynyl pyrimidines or any dNTP containing molecular mass-modifying tags such as those described above), a DNA ligase, and/or reaction buffer, or any combination thereof, for the amplification processes described above. A kit may further include instructions pertinent for the particular embodiment of the kit, such instructions describing the primer pairs and amplification conditions for operation of the method. A kit may also comprise amplification reaction containers such as microcentrifuge tubes and the like. A kit may also comprise reagents or other materials for isolating bioagent nucleic acid or bioagent identifying amplicons from amplification, including, for example, detergents, solvents, or ion exchange resins which may be linked to magnetic beads. A kit may also comprise a table of measured or calculated molecular masses and/or base compositions of bioagents using the primer pairs of the kit.

Some embodiments are kits that contain one or more survey bacterial primer pairs represented by primer pair compositions wherein each member of each pair of primers has 70% to 100% sequence identity with the corresponding member from the group of primer pairs represented by any of the primer pairs of Table 5. The survey primer pairs may include broad range primer pairs which hybridize to ribosomal RNA, and may also include division-wide primer pairs which hybridize to housekeeping genes such as rplB, tufb, rpoB, rpoC, valS, and infb, for example.

In some embodiments, a kit may contain one or more survey bacterial primer pairs and one or more triangulation genotyping analysis primer pairs such as the primer pairs of Tables 8, 12, 14, 19, 21, 23, or 24. In some embodiments, the kit may represent a less expansive genotyping analysis but include triangulation genotyping analysis primer pairs for more than one genus or species of bacteria. For example, a kit for surveying nosocomial infections at a health care facility may include, for example, one or more broad range survey primer pairs, one or more division wide primer pairs, one or more Acinetobacter baumannii triangulation genotyping analysis primer pairs and one or more Staphylococcus aureus triangulation genotyping analysis primer pairs. One with ordinary skill will be capable of analyzing in silico amplification data to determine which primer pairs will be able to provide optimal identification resolution for the bacterial bioagents of interest.

In some embodiments, a kit may be assembled for identification of strains of bacteria involved in contamination of food. An example of such a kit embodiment is a kit comprising one or more bacterial survey primer pairs of Table 5 with one or more triangulation genotyping analysis primer pairs of Table 12 which provide strain resolving capabilities for identification of specific strains of Campylobacter jejuni.

Some embodiments of the kits are 96-well or 384-well plates with a plurality of wells containing any or all of the following components: dNTPs, buffer salts, Mg²⁺, betaine, and primer pairs. In some embodiments, a polymerase is also included in the plurality of wells of the 96-well or 384-well plates.

Some embodiments of the kit contain instructions for PCR and mass spectrometry analysis of amplification products obtained using the primer pairs of the kits.

Some embodiments of the kit include a barcode which uniquely identifies the kit and the components contained therein according to production lots and may also include any other information relative to the components such as concentrations, storage temperatures, etc. The barcode may also include analysis information to be read by optical barcode readers and sent to a computer controlling amplification, purification and mass spectrometric measurements. In some embodiments, the barcode provides access to a subset of base compositions in a base composition database which is in digital communication with base composition analysis software such that a base composition measured with primer pairs from a given kit can be compared with known base compositions of bioagent identifying amplicons defined by the primer pairs of that kit.

In some embodiments, the kit contains a database of base compositions of bioagent identifying amplicons defined by the primer pairs of the kit. The database is stored on a convenient computer readable medium such as a compact disk or USB drive, for example.

In some embodiments, the kit includes a computer program stored on a computer formatted medium (such as a compact disk or portable USB disk drive, for example) comprising instructions which direct a processor to analyze data obtained from the use of the primer pairs of the present invention. The instructions of the software transform data related to amplification products into a molecular mass or base composition which is a useful concrete and tangible result used in identification and/or classification of bioagents. In some embodiments, the kits of the present invention contain all of the reagents sufficient to carry out one or more of the methods described herein.

While the present invention has been described with specificity in accordance with certain of its embodiments, the following examples serve only to illustrate the invention and are not intended to limit the same. In order that the invention disclosed herein may be more efficiently understood, examples are provided below. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting the invention in any manner.

EXAMPLES Example 1 Design and Validation of Primers that Define Bioagent Identifying Amplicons for Identification of Bacteria

For design of primers that define bacterial bioagent identifying amplicons, a series of bacterial genome segment sequences were obtained, aligned and scanned for regions where pairs of PCR primers would amplify products of about 45 to about 150 nucleotides in length and distinguish subgroups and/or individual strains from each other by their molecular masses or base compositions. A typical process shown in FIG. 1 is employed for this type of analysis.

A database of expected base compositions for each primer region was generated using an in silico PCR search algorithm, such as (ePCR). An existing RNA structure search algorithm (Macke et al., Nucl. Acids Res., 2001, 29, 4724-4735, which is incorporated herein by reference in its entirety) has been modified to include PCR parameters such as hybridization conditions, mismatches, and thermodynamic calculations (SantaLucia, Proc. Natl. Acad. Sci. U.S.A., 1998, 95, 1460-1465, which is incorporated herein by reference in its entirety). This also provides information on primer specificity of the selected primer pairs.

Table 2 represents a collection of primers (sorted by primer pair number) designed to identify bacteria using the methods described herein. The primer pair number is an in-house database index number. Primer sites were identified on segments of genes, such as, for example, the 16S rRNA gene. The forward or reverse primer name shown in Table 2 indicates the gene region of the bacterial genome to which the primer hybridizes relative to a reference sequence. In Table 2, for example, the forward primer name 16 S_EC_(—)1077_(—)1106_F indicates that the forward primer (_F) hybridizes to residues 1077-1106 of the reference sequence represented by a sequence extraction of coordinates 4033120.4034661 from GenBank gi number 16127994 (as indicated in Table 3). As an additional example: the forward primer name BONTA_X52066_(—)450_(—)473 indicates that the primer hybridizes to residues 450-437 of the gene encoding Clostridium botulinum neurotoxin type A (BoNT/A) represented by GenBank Accession No. X52066 (primer pair name codes appearing in Table 2 are defined in Table 3. One with ordinary skill knows how to obtain individual gene sequences or portions thereof from genomic sequences present in GenBank. In Table 2, Tp=5-propynyluracil; Cp=5-propynylcytosine; *=phosphorothioate linkage; I=inosine. T. GenBank Accession Numbers for reference sequences of bacteria are shown in Table 3 (below). In some cases, the reference sequences are extractions from bacterial genomic sequences or complements thereof. TABLE 2 Primer Pairs for Identification of Bacteria Primer Forward Reverse Pair Forward SEQ Reverse SEQ Number Forward Primer Name Sequence ID NO: Reverse Primer Name Sequence ID NO: 1 16S_EC_1077_1106_F GTGAGATGTTG 134 16S_EC_1175_1195_R GACGTCATCCCCA 809 GGTTAAGTCCC CCTTCCTC GTAACGAG 2 16S_EC_1082_1106_F ATGTTGGGTTA 38 16S_EC_1175_1197_R TTGACGTCATCCC 1398 AGTCCCGCAAC CACCTTCCTC GAG 3 16S_EC_1090_1111_F TTAAGTCCCGC 651 16S_EC_1175_1196_R TGACGTCATCCCC 1159 AACGATCGCAA ACCTTCCTC 4 16S_EC_1222_1241_F GCTACACACGT 114 16_EC_1303_1323_R CGAGTTGCAGACT 787 GCTACAATG GCGATCCG 5 16S_EC_1332_1353_F AAGTCGGAATC 10 16S_EC_1389_1407_R GACGGGCGGTGTG 806 GCTAGTAATCG TACAAG 6 16S_EC_30_54_F TGAACGCTGGT 429 16S_EC_105_126_R TACGCATTACTCA 897 GGCATGCTTAA CCCGTCCGC CAC 7 16S_EC_38_64_F GTGGCATGCCT 136 16S_EC_101_120_R TTACTCACCCGTC 1365 AATACATGCAA CGCCGCT GTCG 8 16S_EC_49_68_F TAACACATGCA 152 16S_EC_104_120_R TTACTCACCCGTC 1364 AGTCGAACG CGCC 9 16S_EC_683_700_F GTGTAGCGGTG 137 16S_EC_774_795_R GTATCTAATCCTG 839 AAATGCG TTTGCTCCC 10 16S_EC_713_732_F AGAACACCGAT 21 16S_EC_789_809_R CGTGGACTACCAG 798 GGCGAAGGC GGTATCTA 11 16S_EC_785_806_F GGATTAGAGAC 118 16S_EC_880_897_R GGCCGTACTCCCC 830 CCTGGTAGTCC AGGCG 12 16S_EC_785_810_F GGATTAGATAC 119 16S_EC_880_897_2_R GGCGTACTCCCC 830 CCTGGTAGTCA AGGCG CACGC 13 16S_EC_789_810_F TAGATACCCTG 206 16S_EC_880_894_R CGTACTCCCCAGG 796 GTAGTCCACGC CG 14 16S_EC_960_981_F TTCGATGCAAC 672 16S_EC_1054_1073_R ACGAGCTGACGAC 735 GCGAAGAACCT AGCCATG 15 16S_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078_R ACGACCACGAGCTG 734 CTTACC ACGAC 16 23S_EC_1826_1843_F CTGACACCTGC 80 23S_EC_1906_1924_R GACCGTTATAGTT 805 CCGGTGC ACGGCC 17 23S_EC_2645_2669_F TCTGTCCCTAG 408 23S_EC_2744_2761_R TGCTTAGATGCTT 1252 TACGAGAGGAC TCAGC CGG 18 23S_EC_2645_2669_2_F CTGTCCCTAGT 83 23S_EC_2751_2767_R GTTTCATGCTTAG 846 ACGAGAGGACC ATGCTTTCAGC GG 19 23S_EC_493_518_F GGGGAGTGAAA 125 23S_EC_551_571_R ACAAAAGGTACGC 717 GAGATCCTGAA CGTCACCC ACCG 20 23S_EC_493_518_2_F GGGGAGTGAAA 125 23S_EC_551_571_2_R ACAAAAGGCACGC 716 GAGATCCTGAA CATCACCC ACCG 21 23S_EC_971_992_F CGAGAGGGAAA 66 23S_EC_1059_1077_R TGGCTGCTTCTAA 1282 CAACCCAGACC GCCAAC 22 CAPC_BA_104_131_F GTTATTTAGCA 139 CAPC_BA_180_205_R TGAATCTTGAAAC 1150 CTCGTTTTTAA ACCATACGTAAC TCAGCC G 23 CAPC_BA_114_133_F ACTCGTTTTTA 20 CAPC_BA_185_205_R TGAATCTTGAAAC 1149 ATCAGCCCG ACCATACG 24 CAPC_BA_274_303_F GATTATTGTTA 109 CAPC_BA_349_376_R GTAACCCTTGTCT 837 TCCTGTTATGC TTGAATTGTATTT CATTTGAG GC 25 CAPC_BA_276_296_F TTATTGTTATC 663 CAPC_BA_358_377_R GGTAACCCTTGTC 834 CTGTTATGCC TTTGAAT 26 CAPC_BA_281_301_F GTTATCCTGTT 138 CAPC_BA_361_378_R TGGTAACCCTTGT 1298 ATGCCATTTG CTTTG 27 CAPC_BA_315_334_F CCGTGGTATTG 59 CAPC_BA_361_378_R TGGTAACCCTTGT 1298 GAGTTATTG TCTTTG 28 CYA_BA_1055_1072_F GAAAGAGTTCG 92 CYA_BA_1112_1130_R TGTTGACCATGCT 1352 GATTGGG TCTTAG 29 CYA_BA_1349_1370_F ACAACGAAGTA 12 CYA_BA_1447_1426_R CTTCTACATTTTT 800 CAATACAAGAC AGCCATCAC 30 CYA_BA_1353_1379_F CGAAGTACAAT 64 CYA_BA_1448_1467_R TGTTAACGGCTTC 1342 ACAAGACAAAA AAGACCC GAAGG 31 CYA_BA_1359_1379_F ACAATACAAGA 13 CYA_BA_1447_1461_R CGGCTTCAAGACC 794 CAAAAGAAGG CC 32 CYA_BA_914_937_F CAGGTTTAGTA 53 CYA_BA_999_1026_R ACCACTTTTAATA 728 CCAGAACATG AGGTTTGTAGCTA CAGAC 33 CYA_BA_916_935_F GGTTTAGTACC 131 CYA_BA_1003_1025_R CCACTTTTAATAA 768 AGAACATGC GGTTTGTAGC 34 INFB_EC_1365_1393_F TGCTCGTGGTG 524 INFB_EC_1439_1467_R TGCTGCTTTCGCA 1248 CACAAGTAACG TGGTTAATTGCTT GAT ATTA CAA 35 LEF_BA_1033_1052_F TCAAGAAGAAA 254 LEF_BA_1119_1135_R GAATATCAATTTG 803 AAGAGC TAGC 36 LEF_BA_1036_1066_F CAAGAAGAAAA 44 LEF_BA_1119_1149_R AGATAAAGAATCA 745 AGAGCTTCTAA CGAATATCAATTT AAAGAATAC GTAGC 37 LEF_BA_756_781_F AGCTTTTGCAT 26 LEF_BA_843_872_R TCTTCCAAGGATA 1135 ATTATATCGAG ATTTATTTCTTG CCAC TTCG 38 LEF_BA_758_778_F CTTTTGCATATT 90 LEF_BA_843_865_R AGGATAGATTTAT 748 ATATCGAGC TTCTTGTTCG 39 LEF_BA_795_813_F TTTACAGCTTT 700 LEF_BA_883_900_R TCTTGACAGCATC 1140 ATGCACCG CGTTG 40 LEF_BA_883_899_F CAACGGATGCT 43 LEF_BA_939_958_R CAGATAAAGAATC 762 GGCAAG GCTCCAG 41 PAG_BA_122_142_F CAGAATCAAGT 49 PAG_BA_190_209_R CCTGTAGTAGAAG 781 TCCCAGGGG AGGTAAC 42 PAG_BA_123_145_F AGAATCAAGTT 22 PAG_BA_187_210_R CCCTGTAGTAGAA 774 CCCAGGGGTT GAGGTAACCAC AC 43 PAG_BA_269_287_F AATCTGCTATT 11 PAG_BA_326_344_R TGATTATCAGCGG 1186 TGGTCAGG AAGTAG 44 PAG_BA_655_675_F GAAGGATATAC 93 PAG_BA_755_772_R CCGTGCTCCATTT 778 GGTTGATGTC TTCAG 45 PAG_BA_753_772_F TCCTGAAAAAT 341 PAG_BA_849_868_R TCGGATAAGCTGC 1089 GGAGCACGG CACAAGG 46 PAG_BA_763_781_F TGGAGCACGG 552 PAG_BA_849_868_R TCGGATAAGCTGC 1089 CTTCTGATC CACAAGG 47 RPOC_EC_1018_1045_F CAAACTTATTA 39 RPOC_EC_1095_1124_R TCAAGCGCCATTT 959 AGGTAAGCGTG CTTTTGGTAAACC TTGACT ACAT 48 RPOC_EC_1018_1045_2_F CAAAACTTATT 39 RPOC_EC_1095_1124_2_R TCAAGCGCCATCT 958 AGGTAAGCGTG CTTTCGGTAATCC TTGACT ACAT 49 RPOC_EC_114_140_F TAAGAAGCCGG 158 RPOC_EC_213_232_R GGCGCTTGTACTT 831 AAACCATCAAC ACCGCAC TACCG 50 RPOC_EC_2178_2196_F TGATTCTGGTG 478 RPOC_EC_2225_2246_R TTGGCCATCAGGC 1414 CCCGTGGT CACGCATAC 51 RPOC_EC_2178_2196_2_F TGATTCCGGTG 477 RPOC_EC_2225_2246_2_R TTGGCCATCAGAC 1413 CCCGTGGT CACGCATAC 52 RPOC_EC_2218_2241_F CTGGCAGGTAT 81 RPOC_EC_2313_2337_R CGACCGTGGGTT 790 GCGTGGTCTGA GAGATGAAGTAC TG 53 RPOC_EC_2218_2241_2_F CTTGCTGGTAT 86 RPOC_EC_2313_2337_2_R CGCACCATGCGTA 789 GCGTGGTCTGA GAGATGAAGTAC TG 54 RPOC_EC_808_833_F CGTCGGGTGAT 75 RPOC_EC_865_889_R GTTTTTCGTTGCG 847 TAACCGTAACA TACGATGATGTC ACCG 55 RPOC_EC_808_833_2_F CGTCGTGTAAT 76 RPOC_EC_865_891_R ACGTTTTTCGTTT 741 AACCGTAACA TGAACGATAATGC ACCG T 56 RPOC_EC_993_1019_F CAAAGGTAAGC 41 RPOC_EC_1036_1059_R CGAACGGCCTGAG 785 AAGGTCGTTTC TAGTCAACACG CGTCA 57 RPOC_EC_993_1019_2_F CAAAGGTAAGC 40 RPOC_EC_1036_1059_2_R CGAACGGCCAGAG 784 AAGGACGTTTC TAGTCAACACG CGTCA 58 SSPE_BA_115_137_F CAAGCAAACGC 45 SSPE_BA_197_222_R TGCACGTCTGTTT 1201 ACAATCAGAA CAGTTGCAAATTC GC 59 TUFB_EC_239_259_F TAGACTGCCCA 204 TUFB_EC_283_303_R GCCGTCCATCTGA 815 GGACACGCTG GCAGCACC 60 TUFB_EC_239_259_2_F TTGACTGCCCA 678 TUFB_EC__283 _303_2_R GCCGTCCATTTGA 816 GGTCACGCTG GCAGCACC 61 TUFB_EC_976_1000_F AACTACCGTC 4 TUFB_EC_1045_1068_R GTTGTCGCCAGGC 845 CGCAGTTCTAC ATAACCATTTC TTCC 62 TUFB_EC_976_1000_2_F AACTACCGTCC 5 TUFB_EC_1045_1068_2_R GTTGTCACCAGGC 844 TCAGTTCTACT ATTACCATTTC TCC 63 TUFB_ECG_985_1012_F CCACAGTTCTA 56 TUFB_EC_1033_1062_R TCCAGGCATTACC 1006 CTTCCGTACTA ATTTCTACTCCTT CTGACG CTGG 66 RPLB_EC_650_679_F GACCTACAGTA 98 RPLB_E739_762_R TCCAAGTGCTGGT 999 AGAGGTTCTGT TTACCCCATGG AATTGAACC 67 RPLB_EC_688_710_F CATCCACACGG 54 RFLB_EC_736_757_R GTGCTGGTTTACC 842 TGGTGGTGAAG CCATGGAGT G 68 RPOC_EC_1036_1060_F CGTGTTGACTA 78 RPOC_EC_1097_1126_R ATTCAAGAGCCAT 754 TTCGGGGCGTTC TTCTTTTGGTAAA AG CCAC 69 RPOB_EC_3762_3790_F TCAACAACCTC 248 RPOB_EC_3836_3865_R TTTCTTGAAGAGT 1435 TTGGAGGTAAA ATGAGCTGCTCCG GCTCAGT TAAG 70 RPLB_EC_688_710_F CATCCACACGG 54 RPLB_EC_743_771_R TGTTTTGTATCCA 1356 TGGTGGTGAAG AGTGCTGGTTTAC G CCC 71 VALS_EC_1105_1124_F CGTGGCGGCGT 77 VALS_EC_1195_1218_R CGGTACGAACTGG 795 GGTTATCGA ATGTCGCCGTT 72 RPOB_EC_1845_1866_F TATCGCTCAGG 233 RFOB_EC_1909_1929_R GCTGGATTCGCCT 825 CGAACTCCAAC TTGCTACG 73 RPLB_EC_669_698_F TGTAATGAACC 623 RPLB_BC_735_761_R CCAAGTGCTGGTT 767 CTAATGACCAT TACCCCATGGAGT CCACACGG A 74 RPLB_EC_671_700_F TAATGAACCCT 169 RPLB_EC_737_762_R TCCAAGTGCTGGT 1000 AATGACCATCC TTACCCCATGGAG 75 SP101_SPET11_1_29_F AACCTTAATTG 2 SP101_SPET11_92_116_R CCTACCCAACGTT 779 GAAAGAAACCC CACCAAGGGCAG AAGAAGT 76 SP101_SPET11_118_147_F GCTGGTGAAAA 115 SP101_SPET11_213_238_R TGTGGCCGATTTC 1340 TAACCCAGATG ACCACCTGCTCCT TCGTCTTC 77 SP101_SPET11_216_243_F AGCAGGTGGTG 24 SP101_SPET11_308_333_R TGCCACTTTGACA 1209 AAATCGGCCAC ACTCCTGTTGCTG ATGATT 78 SP101_SPET11_266_295_F CTTGTACTTGT 89 SP101_SFET11_355_380_R GCTGCTTTGATGG 824 GGCTCACACGG CTGAATCCCCTTC CTGTTTGG 79 SP101_SPET11_322_344_F GTCAAAGTGGC 132 SF101SFET11_423_441R ATCCCTGCTTCT 753 CACGTTTACTG GCTGCC GC 80 SP101_SPET11_358_387_F GGGGATTCAGC 126 SP101_SPET11_448_473_R CCAACCTTTTCCA 766 CATCAAAGCAG CAACAGAATCAGC CTATTGAC 81 SP101_SPET11_600_629_F CCTTACTTCGA 62 SP101_SPET11_686_714_R CCCATTTTTTCAC 772 AACTATGAATC GCATGCTGAAAAT TTTTGGAAG ATC 82 SP101_SPET11_658_684_F GGGGATTGATA 127 SP101_SPET11_756_784_R GATTGGCGATAAA 813 TCACCATAAG GTGATATTTTCTA AAGAA AAA 83 SP101_SPET11_776_801_F TCGCCAATCAA 364 SP101_SPET11_871_896_R GCCCACCAGAAAG 814 AACTAAGGGAA ACTAGCAGGATAA TGGC 84 SP101_SPET11_893_921_F GGGCAACAGCA 123 SP101_SPET11_988_1012_R CATGACAGCCAAG 763 GCGGATTGCGA ACCTCACCCACC TTGCGCG 85 SP101_SPET11_1154_1179_F CAATACCGCAA 47 SP101_SPET11_1251_1277_R GACCCCAACCTGG 804 CAGCGGTGGCT CCTTTTGTCGTTG TGGG A 86 SP101_SPET11_1314_1336_F CGCAAAAAAAT 68 SP101_SPET11_1403_1431_R AAACTATTTTTTT 711 CCAGCTATTAG AGCTATACTCGAA C CAC 87 SP101_SPET11_1408_1437_F CGAGTATAGCT 67 SP101_SPET11_1486_1515_R GGATAATTGGTCG 828 AAAAAAATAGT TAACAAGGGATAG TTATGACA TGAG 88 SP101_SPET11_1688_1716_F CCTATATTAAT 60 SP101_SPET11_1783_1808_R ATATGATTATCAT 752 CGTTTACAGAA TGAACTGCGGCCG ACTGGCT 89 SP101_SPET11_1711_1733_F CTGGCTAAAA 82 SP101_SPET11_1808_1835_R GCGTGACAGACCT 821 CTTTGGCAAC TCTTGAATTGTAA GG TCA 90 SP101_SPET11_1807_1835_F ATGATTACAAT 33 SP101_SPET11_1901_1927_R TTGGACCTGTAAT 1412 TCAAGAAGGTC CAGCTGAATACTG GTCACGC G 91 SP101_SPET11_1967_1991_F TAACGGTTATC 155 SP101_SPET11_2062_2083_R ATTGCCCAGAAAT 755 ATGGCCCAGAT CAAATCATC GGG 92 SP101_SPET11_2260_2283_F CAGAGACCGTT 50 SP101_SPET11_2375_2397_R TCTGGGTGACCTG 1131 TTATCCTATCA GTGTTTTAGA GC 93 S9101_SPET11_2375_2399_F TCTAAAACACC 390 SP101_SPET11_2470_2497_R AGCTGCTAGATGA 747 AGGTCACCCAG GCTTCTGCCATGG AAG CC 94 SF101_SPET11_2468_2487_F ATGGCCATGGC 35 SP101_SPET11_2543_2570_R CCATAAGGTCACC 770 AGAAGCTCA GTCACCATTCAAA GC 95 SP101_SPET11_2961_2984_F ACCATGACAGA 15 SP101_SPET11_3023_3045_R GGAATTTACCAGC 827 AGGCATTTTGA GATAGACACC CA 96 SP101_SPET11_3075_3103_F GATGACTTTTT 108 SP101_SPET11_3168_3196_R AATCGACGACCAT 715 AGCTAATGGTC CTTGGAAAGATTT AGGCAGC CTC 97 SP101_SPET11_3386_3403_F AGCGTAAAGGT 25 SP101_SPET11_3480_3506_R CCAGCAGTTACTG 769 GAACCTT TCCCCTCATCTTT G 98 SP101_SPET11_3511_3535_F GCTTCAGGAAT 116 SP101_SPET11_3605_3629_R GGGTCTACACCTG 832 CAATGATGGAG CACTTGCATAAC CAG 111 RPOB_EC_3775_3803_F CTTGGAGGTAA 87 RFOB_EC_3829_3858_R CGTATAAGCTGCA 797 GTCTCATTTTG CCATAAGCTTGTA GTGGGCA ATGC 112 VALS_EC_1833_1850_F CGACGCGCTGC 65 VALS_EC_1920_1943_R GCGTTCCACAGCT 822 GCTTCAC TGTTGCAGAAG 113 RPOB_EC_1336_1353_F GACCACCTCGG 97 RPOB_EC_1438_1455_R TTCGCTCTCGGCC 1386 CAACCGTA TGGCC 114 TUFB_EC_225_251_F GCACTATGCAC 111 TUFB_EC_284_309_R TATAGCACCATCC 930 ACGTAGATTGT ATCTGAGCGGCAC CCTGG 115 DNAK_EC_428_449_F CGGCGTACTTC 72 DNAK_EC_503_522_R CGCGGTCGGCTCG 792 AACGACAGCCA TTGATGA 116 VALS_EC_1920_1943_F CTTCTGCAACA 85 VALS_EC_1948_1970_R TCGCAGTTCATCA 1075 AGCTGTGGAAC GCACGAAGCG GC 117 TUFB_EC_757_474_F AAGACGACCTG 6 TUFB_EC_849_867_R GCGCTCCACGTCT 819 CACGGGC TCACGC 118 23S_EC_2646_2667_F CTGTTCTTAGT 84 23S_EC_2745_2765_R TTCGTGCTTAGAT 1389 ACGAGAGGACC GCTTTCAG 119 16S_EC_969_985_1P_F ACGCGAAGAC 19 16S_EC_1061_1078_2P_R ACGACACGAGCpT 733 CTTACpC pGACGAC 120 16S_EC_972_985_2P_F CGAAGAACpCp 63 16S_EC_1064_1075_2P_R ACACGAGCpTpGA 727 TTACC C 121 16S_EC_972_985_F CGAAGAACCTT 63 16S_EC_1064_1075_R ACACGAGCTGAC 727 ACC 122 TRAN_ILE- CCTGATAAGGG 61 23S_SC_40_59_R ACGTCCTTCATCG 740 RRNH_EC_32_50.2_F CCTCTGA 123 23S_EC_−7_15_F GTTGTGAGGTT 140 23S_EC_430_450_R CTATCGGTCAGTC 799 AAGCGACTAAG AGGAGTAT 124 23S_EC_−7_15_F GTTGTGAGGTT 141 23S_EC_891_910_R TTGCATCGGGTTG 1403 AAGCGACTAAG GTAAGTC 125 23S_EC_430_450_F ATACTCCTGAC 30 23S_EC_1424_1442_R AACATAGCCTTCT 712 TGACCGATAG CCGTCC 126 23S_EC_891_910_F GACTTACCAAC 100 23S_SC_1908_1931_R TACCTTAGGACCG 893 CCGATGCAA TTATAGTTACG 127 23S_EC_1424_1442_F GGACGGAGAAG 117 23S_EC_2475_2494_R CCAAACACCGCCG 765 GCTATGTT TCGATAT 128 23S_EC_1908_1931_F CGTAACTATAA 73 23S_EC_2833_9852_R GCTTACACACCCG 826 CGGTCCTAAGG GCCTATC TA 129 23S_EC_2475_9494_F ATATCGACGGC 31 TRNA_ASP- GCGTGACAGGCAG 820 GGTGTTTGG RRNH_EC_23_41.2_R GTATTC 131 16S_EC_−60_−39_F AGTCTCAAGAG 28 16S_EC_508_525_R GCTGCTGGCACGG 823 TGAACACGTAA AGTTA 132 16S_EC_326_345_F GACACGGTCCA 95 16S_EC_1041_1058_R CCATGCAGCACCT 771 GACTCCTAC GTCTC 133 16S_EC905_724_F GATCTGGAGGA 107 16S_EC_1493_3512_R ACGGTTACCTTGT 739 ATACCGGTG TACGACT 134 16S_EC_1268_1287_F GAGAGCAAGCG 101 TRNA_ALA- CCTCCTGCGTGCA 780 GACCTCATA RRNH_EC_30_40.2_R AAGC 135 16S_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_R ACAACACGAGCTG 719 CTTACC ACGAC 137 165_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_I14_R ACAACACGAGCTG 721 CCTTACC ICGAC 138 165_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_107.2_I12_R ACAACACGAGCIG 718 CTTACC CGAC 139 16S_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_I11_R ACAACACGAGITG 722 CTTACC ACGAC 140 16S_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_I16_R ACAACACGAGCTG 720 CTTACC ACIAC 141 16S_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_2I_R ACAACACGAICTI 723 CTTACC ACGAC 142 165_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_3I_R ACAACACIAICTI 724 CTTACC ACGAC 143 16S_EC_99_985_F ACGCGAAGAAC 19 16S_EC_1061_1078.2_4I_R ACACCACIAICTI 725 CTTACC ACIAC 147 23S_EC_2652_2669_F CTAGTACGAGA 79 23S_EC_2741_2760_R ACTTAGATGCTTT 743 GGACCGG CAGCGGT 158 16S_EC_683_700_F GTGTAGCGGTG 137 16S_EC_880_894_R CGTACTCCCCAGG 796 AAATGCG CG 159 16S_EC_1100_1116_F CAACGAGCGCA 42 16S_EC_1174_1188_R TCCCCACCTTCCT 1019 ACCCTT CC 215 SSPE_BA_121_137_F AACGCACAATC 3 SSPE_BA_197_216_R TCTGTTTCAGTTG 1132 AGAAGC CAAATTC 220 GROL_EC_941_959_F TGGAAGATCTG 544 GROL_EC_1039_1060_R CAATCTGCTGACG 759 GGTCAGGC GATCTGAGC 221 INFB_EC_1103_1124_F GTCGTGAAAAC 133 INFB_EC_1174_1191_R CATGATGGTCACA 764 GAGCTGGAAGA ACCGG 222 HFLB_EC_1082_1102_F TGGCGAACCTG 569 HFLB_EC_1144_1168_R CTTTCGCTTTCTC 802 GTGAACGAAGC GAACTCAACCAT 223 INFB_EC_1969_1994_F CGTCAGGGTAA 74 INFB_EC_2038_2058_R AACTTCGCCTTCG 713 ATTCCGTGAAG GTCATGTT TTAA 224 GROL_EC_219_242_F GGTGAAAGAAG 128 GROL_EC_328_350_R TTCAGGTCCATCG 1377 TTGCCCTCTAA GGTTCATGCC AGC 225 VALS_EC_1105_1124_F CGTGGCGGCGT 77 VALS_EC_1195_1214_R ACGAACTGGATGT 732 GGTTATCGA CGCCGTT 226 16S_EC_556_575_F CGGAATTACTG 70 16S_EC_683_700_R CGCATTTCACCGC 791 GGCGTAAAG TACAC 227 RPOC_EC_1256_1277_F ACCCAGTGCTG 16 RPOC_EC_1295_1315_R GTTCAAATGCCTG 843 CTGAACCGTGC GATACCCA 228 16S_EC_774_795_F GGGAGCAAACA 122 16S_EC_880_894_R CGTACTCCCCAGG 796 GGATTAGATAC CG 229 RPOC_EC_1584_1604_F TGGCCCGAAAG 567 RPOC_EC_1623_1643_R ACGCGGGCATGCA 737 AAGCTGAGCG GAGATGCC 230 16S_EC_1082_1100_F ATGTTGGGTTA 37 16S_EC_1177_1196_R TGACGTCATCCCC 1158 AGTCCCGC ACCTTCC 231 16S_EC_1389_1407_F CTTGTACACAC 88 16S_EC_1525_1541_R AAGGAGGTGATCC 714 CGCCCGTC AGCC 232 16S_EC_1303_1323_F CGGATTGGAGT 71 16S_EC_1389_1407_R GACGGCGGTGTG 808 CTGCAACTCG TACAAG 233 23S_EC_23_37_F GGTGGATGCCT 129 23S_EC_115_130_R GGGTTTCCCCATT 833 TGGC CGG 234 23S_EC_187_207_F GGGAACTGAAA 121 23S_EC_242_256_R TTCGCTCGCCGCT 1385 CATCTAAGTA AC 235 23S_EC_1602_1620_F TACCCCAAACC 184 23S_EC_1686_1703_R CCTTCTCCCGAAG 782 GACACAGG TTACG 236 23S_EC_1685_1703_F CCGTAACTTC 58 23S_EC_1828_1842_R CACCGGGCAGGCG 760 GGAGAAGG TC 237 23S_EC_1827_1843_F GACGCCTGCCC 99 23S_EC_1929_1949_R CCGACAAGGAATT 775 GGTGC TCGCTACC 238 23S_EC_2434_2456_F AAGGTACTCCG 9 23S_EC_9490_2511_R AGCCGACATCGAG 746 GGGATAACAGG GGTGCCAAAC C 239 23S_EC_2599_2616_F GACAGTTCGGT 96 23S_SC_2653_2669_R CCGGTCCTCTCGT 777 CCCTATC ACTA 240 23S_EC_2653_2669_F TAGTACGAGAG 227 23S_EC_2737_2758_R TTAGATGCTTTCA 1369 GACCGG GCACTTATC 241 23S_ES_−68_−44_F AAACTAGATAA 1 23S_B_5_21_R GTGCGCCCTTTCT 841 CAGTAGACATC AACTT AC 242 16S_EC_8_27_F AGAGTTTGATC 23 16S_SC_342_358_R ACTGCTGCCTCCC 742 ATGGCTCAG GTAG 243 16S_EC_314_332_F CACTGGAACTG 48 16S_EC_556_575_R CTTTACGCCCAGT 801 AGACACGG AATTCCG 244 16S_EC_518_536_F CCAGCAGCCGC 57 16S_EC_774_795_R GTATCTAATCCTG 839 GGTAATAC TTTGCTCCC 245 16S_EC_683_700_F GTGTAGCGGTG 137 16S_EC_967_985_R GGTAAGGTTCTTC 835 AAATGCG GCGTTG 246 16S_EC_937_954_F AAGCGGTGGAG 7 16S_EC_1220_1240_R ATTGTAGCACGTG 757 CATGTGG TGTAGCCC 247 16S_EC_1195_1213_F CAAGTCATCAT 46 16S_EC_1525_1541_R AAGGAGGTGATCC 714 GGCCCTTA AGCC 248 16S_EC_8_27_F AGAGTTTGATC 23 16S_EC_1525_1541_R AAGGAGGTGATCC 714 ATGGCTCAG AGCC 249 23S_EC_1831_1849_F ACCTGCCCAGT 18 23S_EC_1919_1936_R TCGCTACCTTAGG 1080 GCTGGAAG ACCGT 250 16S_EC_1387_1407_F GCCTTGTACAC 112 16S_EC_1494_1513_R CACGGCTACCTTG 761 ACCTCCCGTC TTACGAC 251 16S_EC_1390_1411_F TTGTACACACC 693 16S_EC_1486_1505_R CCTTGTTACGACT 783 GCCCGTCATAC TCACCCC 252 16S_EC_1367_1387_F TACGGTGAATA 191 16S_EC_1485_1506_R ACCTTGTTACGAC 731 CGTTCCCGGG TTCACCCCA 253 16S_EC_804_822_F ACCACGCCGTA 14 16S_EC_909_929_R CCCCCGTCAATTC 773 AACGATGA CTTTGAGT 254 16S_EC_791_812_F GATACCCTGGT 106 16S_EC_886_04_R GCCTTGCGACCGT 817 AGTCCACACCG ACTCCC 255 16S_EC_789_810_F TAGATACCCTG 206 16S_EC_882_899_R GCGACCGTACTCC 818 GTAGTCCACGC CCAGG 256 16S_EC_1092_1109_F TAGTCCCGCAA 228 16S_EC_1174_1195_R GACGTCATCCCCA 810 CGAGCGC CCTTCCTCC 257 23S_EC_2586_2607_F TAGAACGTCGC 203 23S_EC_2658_2677_R AGTCCATCCCGGT 749 GAGACAGTTCG CCTCTCG 258 RNASEP_SA_31_49_F GAGGAAAGTCC 103 RNASEP_SA_358_379_R ATAAGCCATGTTC 750 ATGCTCAC TGTTCCATC 258 RNASEP_SA_31_49_F GAGGAAAGTCC 103 RNASEP_EC_345_362_R ATAAGCCGGGTTC 751 ATGCTCAC TGTCG 258 RNASEP_SA_31_49_F GAGGAAAGTCC 103 RNASEP_BS_363_384_R GTAAGCCATGTTT 838 ATGCTCAC TGTTCCATC 258 RNASEP_BS_43_61_F GAGGAAAGTCC 104 RNASEP_SA_358_379_R ATAAGCCATGTTC 750 ATGCTCGC TGTTCCATC 258 RNASEP_BS_43_61_F GAGGAAAGTCC 104 RNASEP_EC_345_362_R ATAAGCCGGGTTC 751 ATGCTCGC TGTCG 258 RNASEP_BS_43_31_F GAGGAAAGTCC 104 RNASEP_ES_363_384_R GTAAGCCATGTTT 838 ATGCTCGC TGTTCCATC 258 RNASEP_EC_61_77_F GAGGAAAGTCC 105 RNASEP_SA_358_379_R ATAAGCCATGTTC 750 GGGCTC TGTTCCATC 258 RNASEP_EC_61_77_F GAGGAAAGTCC 105 RNASEP_EC_345_362_R ATAAGCCGGGTTC 751 GGGCTC TGTCG 258 RNASEP_EC_61_77_F GAGGAAAGTCC 105 RNASEP_BS_363_384_R GTAAGCCATGTTT 838 GGGCTC TGTTCCATC 259 RNASEP_ES_4331_F GAGGAAAGTCC 104 RNASEP_ES_363_384_R GTAAGCCATGTTT 838 ATGCTCGC TGTTCCATC 260 RNASEP_EC_61_77_F GAGGAAAGTCC 105 RNASEP_EC_345_362_R ATAAGCCGGGTTC 751 GGGCTC TGTCG 262 RNASEP_SA_31_49_F GAGGAAAGTCC 103 RNASEP_SA_358_379_R ATAAGCCATGTTC 750 ATGCTCAC TGTTCCATC 263 16S_EC_1082_1100_F ATGTTGGGTTA 37 16S_EC_1525_1541_R AAGGAGGTGATCC 714 AGTCCCGC AGCC 264 16S_EC_556_575_F CGGAATTACTG 70 16S_EC_774_795_R GTATCTAATCCTG 839 GGCGTAAAG TTGCTCCC 265 16S_EC_1082_1100_F ATGTTGGGTTA 37 16S_EC_1177_1196_10G_R TGACGCATGCCC 1160 AGTCCCGC ACCTTCC 266 16S_EC_1082_1100_F ATGTTGGGTTA 37 16S_EC_1177_1196_10G_11G_R TGACGTCATGGCC 1161 AGTCCCGC ACCTTCC 268 YAED_EC_513_532_F_MOD GGTGTTAAATA 130 TRNA_ALA- AGACCTCCTGCGT 744 GCCTGGCAG RRNA_EC_30_49_F_MOD GCAAAGC 269 16S_EC_1082_1100_F_MOD ATGTTGGGTTA 37 16S_EC_1177_1196_R_MOD TGACGCATCCCC 1158 AGTCCCGC ACCTTCC 270 23S_EC_2586_2607_F_MOD TAGAACGTCGC 203 23S_EC_2658_2677_R_MOD AGTCCATCCCGGT 749 GAGACAGTTCG CCTCTCG 272 16S_EC_969_985_F ACGCGAAGAAC 19 16S_EC_1389_1407_R GACGGGCGGTGTG 807 CTTACC TACAAG 273 16S_EC_683_700_F GTGTAGCGGTG 137 16S_EC_1303_1323_R CGAGTTGCAGACT 788 AAATGCG GCGATCCG 274 169_EC_49_68_F TAACACATGCA 152 16S_EC_880_894_R CGTACTCCCCAGG 796 AGTCGAACG CG 275 16S_EC_49_68_F TAACACATGCA 152 16S_EC_1061_1078_R ACGACACGAGCTG 734 AGTCGAACG ACGAC 277 CYA_BA_1349_1370_F ACAACGAAGTA 12 CYA_BA_1426_1447_R CTTCTACATTTTT 800 CAATACAAGAC AGCCATCAC 278 16S_EC_1090_1111_2_F TTAAGTCCCGC 650 16S_EC_1175_1196_R TGACGTCATCCCC 1159 AACGAGCGCAA ACCTTCCTC 279 16S_EC_405_432_F TGAGTGATGAA 464 16S_EC_507_527_R CGGCTGCTGGCAC 793 GGCCTTAGGGT GAAGTTAG TGTAAA 280 GROL_EC_496_518_F ATGGACAAGGT 34 GROL_EC_577_596_R TAGCCGCGGTCGA 914 TGGCAAGGAAG ATTGCAT G 281 GROL_EC_511_536_F AAGGAAGGCGT 8 GROL_EC_571_593_R CCGCGGTCGAATT 776 GATCACCGTTG GCATGCCTTC AAGA 288 RPOB_EC_3802_3821_F CAGCGTTTCGG 51 RPOB_EC_3862_3885_R CGACTTGACGGTT 786 CGAAATGGA AACATTTCCTG 289 RPOB_EC_3799_3821_F GGGCAGCGTTT 124 RPOB_EC_3862_3888_R GTCCGACTTGACG 840 CGGCGAAATG GTCAACATTTCCT GA G 290 RPOC_EC_2146_2174_F CAGGAGTCGTT 52 RPOC_EC_2227_2245_R ACGCCATCAGGCC 736 CAACTCGATCT ACGCAT ACATGAT 291 ASPS_EC_405_422_F GCACAACCTGC 110 ASPS_EC_521_538_R ACGGCACGAGGTA 738 GGCTGCG GTCGC 292 RPOC_EC_1374_1393_F CGCCGACTTCG 69 RPOC_EC_1437_1455_R GAGCATCAGCGTG 811 ACGGTGACC CGTGCT 293 TUFB_EC_957_979_F CCACACGCCGT 55 TUFB_EC_1034_1058_R GGCATCACCATTT 829 TCTTCAACAAC CCTTGTCCTTCG T 294 16S_EC_7_33_F GAGAGTTTGAT 102 16S_EC_101_122_R TGTTACTCACCCG 1345 CCTGGCTCAGA TCTGCCACT ACGAA 295 VALS_EC_610_649_F ACCGAGCAAGG 17 VALS_EC_705_727_R TATAACGCACATC 929 AGACCAGC GTCAGGGTGA 344 16S_EC_971_990_F GCGAAGAACCT 113 16S_EC_1043_1062_R ACAACCATGCACC 726 TACCAGGTC ACCTGTC 346 16S_EC_713_732_TMOD_F TAGAACACCGA 202 16S_EC_789_809_TMOD_R TCGTGGACTACCA 1110 TGGCGAAGGC GGGTATCTA 347 16S_EC_785_806_TMOD_F TGGATTAGAGA 560 16S_EC_880_897_TMOD_R TGGCCGTACTCCC 1278 CCCTGGTAGTC CAGGCG C 348 16S_EC_960_981_TMOD_F TTTCGATGCAA 706 16S_EC_1054_1073_TMOD_R TACGAGCTGACGA 895 CGCGAAGAACC CAGCCATG T 349 23S_EC_1826_1843_TMOD_F TCTGACACCTG 401 23S_EC_1906_1924_TMOD_R TGACCGTTATAGT 1156 CCCGGTGC TACGGCC 350 CAPC_BA_274_303_TMOD_F TGATTATTGTT 476 CAPC_BA_349_376_TMOD_R TGTAACCCTTGTC 1314 ATCCTGTTATG TTTGAATTGTAT CCATTTGAG TGC 351 CYA_BA_1353_1379_TMOD_F TCGAAGTACAA 355 CYA_BA_1448_1467_TMOD_R TTGTTAACGGCTT 1423 TACAAGACAAA CAAGACCC AGAAGG 352 INFB_EC_1365_1393_TMOD_F TTGCTCGTGGT 687 INFB_EC_1439_1467_TMOD_R TTGCTGCTTTCGC 1411 GCACAAGTAAC ATGGTTAATTGCT GGATATTA TCAA 353 LEF_BA_756_781_TMOD_F TAGCTTTTGCA 220 LEF_BA_843_872_TMOD_R TTCTTCCAAGGAT 1394 TATTATATCGA AGATTTATTTCTT GCCAC GTTCG 354 RPOC_EC_2218_2241_TMOD_F TCTGGCAGGTA 405 RPOC_EC_2313_2337_TMOD_R TCGCACCGTGGGT 1072 TGCGTGGTCTG TGAGATGAAGTAC ATG 355 SSPE_BA_115_137_TMOD_F TCAAGCAAACG 255 SSPE_BA_197_222_TMOD_R TTGCACGTCTGTT 1402 CACAATCAGAA TCAGTTGCAAATT GC C 356 RPLB_EC_650_679_TMOD_F TGACCTACAGT 449 RPLB_EC_739_762_TMOD_R TTCCAAGTGCTGG 1380 AAGAGGTTCTG TTTACCCCATGG TAATGAACC 357 RPLB_EC_688_710_TMOD_F TCATCCACACG 296 RPLB_EC_736_757_TMOD_R TGTGCTGGTTTAC 1337 GTGGTGGTGAA CCCATGGAGT GG 358 VALS_EC_1105_1124_TMOD_F TCGTGGCGGCG 385 VALS_EC_1195_1218_TMOD_R TCGGTACGAACTG 1093 TGGTTATCGA GATGTCGCCGTT 359 RPOB_EC_1845_1866_TMOD_F TTATCGCTCAG 659 RPOB_EC_1909_1929_TMOD_R TGCTGGATTCGCC 1250 GCGAACTCCAA TTTGCTACG C 360 23SEC_2646_2667_TMOD_F TCTGTTCTTAG 409 23S_EC_2745_2765_TMOD_R TTTCGTGCTTAGA 1434 TACGAGAGGAC TGCTTTCAG C 361 16S_EC_1090_1111_2_TMOD_F TTTAAGTCCCG 697 16S_EC_1175_1196_TMOD_R TTGACGTCATCCC 1398 CAACGAGCGCA CACCTTCCTC A 362 RPOB_EC_3799_3821_TMOD_F TGGGCAGCGTT 581 RPOB_EC_3862_3888_TMOD_R TGTCCGACTTGAC 1325 TCGGCGAAATG GGTCAACATTTCC GA TG 363 RPOC_EC_2146_2174_TMOD_F TCAGGAGTCGT 284 EPOC_EC_2227_2245_TMOD_R TACGCCATCAGGC 898 TCAACTCGATC CACGCAT TACATGAT 364 RPOC_EC_1374_1393_TMOD_F TCGCCGACTTC 367 RPOC_EC_1437_1455_TMOD_R TGAGCATCAGCGT 1166 GACGGTGACC GCGTGCT 367 TUFB_ECG_957_979_TMOD_F TCCACACGCCG 308 TUFB_EC_1034_1058_TMOD_R TGGCATCACCATT 1276 TTCTTCAACAA TCCTTGTCCTTCG CT 423 SP101_SPET11_893_921_TMOD_F TGGGCAACAGC 580 SP101_SPET11_988_1012_TMOD_R TCATGACAGCCAA 990 AGCGGATTGCG GACCTCACCCACC ATTGCGCG 424 SP101_SPET11_1154_1179_(—) TCAATACCGCA 258 SP101_SPET11_1251_1277_TMOD_R TGACCCCAACCTG 1155 TMOD_F ACAGCGGTGGC GCCTTTTGTCGTT TTGGG GA 425 SP101_SPET11_118_147_TMOD_F TGCTGGTGAAA 528 SP101_SPET11_213_238_TMOD_R TTGTGGCCGATTT 1422 ATAACCCAGAT CACCACCTGCTCC GTCGTCTTC T 426 SP101_SPET11_1314_1336_TMOD_F TCGCAAAAAAA 363 SP101_SPET11_1403_1431_TMOD_R TAAACTATTTTTT 849 TCCAGCTATTA TAGCTATACTCGA GC ACAC 427 SP101_SPET11_1408_1437_(—) TCGAGTATAGC 359 SP101_SPET11_1486_1515_TMOD_R TGGATAATTGGTC 1268 TMOD_F TTAAAAAAATA GTAACAAGGGATA GTTTATGACA GTGAG 428 SP101_SPET11_1688_1716_TMOD_F TCCTATATTAA 334 SP101_SPET11_1783_1808_TMOD_R TATATGATTATCA 932 TCGTTTACAGA TTGAACTGCGGCC AACTGGCT G 429 SP101_SPET11_1711_1733_(—) TCTGGCTAAAA 406 SP101_SPET11_1808_1835_TMOD_R TGCGTGACGACCT 1239 TMOD_F CTTTGGCAACG TCTTGAATTGTAA GT TCA 430 SP101_SPET11_1807_1835_TMOD_F TATGATTACAA 235 SP101_SPET11_1901_1927_TMOD_R TTTGGACCTGTAA 1439 TTCAAGAAGGT TCAGCTGAATACT CGTCACGC GG 431 SP101_SPET11_1967_1991_(—) TTAACGGTTAT 649 SP101_SPET11_2082_2083_TMOD_R TATTGCCCAGAAA 940 TMOD_F CATGGCCCAGA TCAAATCATC TGGG 432 SP101_SPET11_216_243_TMOD_F TAGCAGGTGGT 210 SP101_SPET11_308_333_TMOD_R TTGCCACTTTGAC 1404 GAAATCGGCCA AACTCCTGTTGCT CATGATT G 433 SP101_SPET11_2260_2283_(—) TCAGAGACCGT 272 SP101_SPET11_2375_2397_TMOD_R TTCTGGGTGACCT 1393 TMOD_F TTTATCCTATC GGTGTTTTAGA AGC 434 SP101_SPET11_2375_2399_(—) TTCTAAAACAC 675 SP101_SPET11_2470_2497_TMOD_R TAGCTGCTAGATG 918 TMOD_F CAGGTCACCCA AGCTTCTGCCATG GAAG GCC 435 SP101_SPET11_2468_2487_(—) TATGGCCATGG 238 SP101_SPET11_2543_2579_TMOD_R TCCATAAGGTCAC 1007 TMOD_F CAGAAGCTCA CGTCACCATTCAA AGC 436 SP101_SFET11_266_295_TMOD_F TCTTGTACTTG 417 SP101_SPET11_355_380_TMOD_R TGCTGCTTTGATG 1249 TGGCTCACACG GCTGAATCCCCTT GCTGTTTGG C 437 SP101_SPET11_2961_2984_(—) TACCATGACAG 183 SP101_SPET11_3023_3045_TMOD_R TGGAATTTACCAG 1264 TMOD_F AAGGCATTTTG CGATAGACACC ACA 438 SP101_SPET11_3075_3103_(—) TGATGACTTTT 473 SP101_SPET11_3168_3196_TMOD_R TAATCGACGACCA 875 TMOD_F TAGCTAATGGT TCTTGGAAAGATT CAGGCAGC TCTC 439 SP101_SPET11_322_344_TMOD_F TGTCAAAGTGG 631 SP101_SPET11_423_441_TMOD_R TATCCCCTGCTTC 934 CACGTTTACTG TGCTGCC GC 440 SP101_SPET11_3386_3403_(—) TAGCGTAAAGG 215 SP101_SPET11_3480_3506_TMOD_R TCCAGCAGTTACT 1005 TMOD_F TGAACCTT GTCCCCTCATCTT TG 441 SP101_SPET11_3511_3535_(—) TGCTTCAGGAA 531 SP101_SPET11_3605_3629_TMOD_R TGGGTCTACACCT 1294 TMOD_F TCAATGATGGA GCACTTGCATAAC GCAG 442 SP101_SPET11_358_387_TMOD_F TGGGGATTCAG 588 SP101_SPET11_448_473_TMOD_R TCCAACCTTTTCC 998 CCATCAAAGCA ACAACAGAATCAG GCTATTGAC C 443 SP101_SPET11_600_628_TMOD_F TCCTTACTTCG 348 SP101_SPET11_886_714_TMOD_R TCCCATTTTTTCA 1018 AACTATGAATC CGCATGCTGAAAA TTTTGGAAG TATC 444 SP101_SPET11_658_684_TMOD_F TGGGGATTGAT 589 SP101_SPET11_756_784_TMOD_R TGATTGGCGATAA 1189 ATCACCGATAA AGTGATATTTTCT GAAGAA AAAA 445 SP101_SPET11_776_801_TMOD_F TTCGCCAATCA 673 SP101_SPET11_871_896_TMOD_R TGCCCACCAGAAA 1217 AAACTAAGGGA GACTAGCAGGATA ATGGC A 446 SP101_SPET11_1_29_TMOD_F TAACCTTAATT 154 SP101_SPET11_92_116_TMOD_R TCCTACCCAACGT 1044 GGAAAGAAACC TCACCAAGGGCAG CAAGAAGT 447 SP101_SPET11_364_385_F TCAGCCATCAA 276 SP101_SPET11_448_471_R TACCTTTTCCACA 894 AGCAGCTATTG ACAGAATCAGC 448 SP101_SPET11_3085_3104_F TAGCTAATGGT 216 SP101_SPET11_3170_3194_R TCGACGACCATCT 1066 CAGGCAGCC TGGAAAGATTTC 449 RPLB_EC_990_710_F TCCACACGGTG 309 RPLB_EC_737_758_R TGTGCTGGTTTAC 1336 GTGGTGAAGG CCCATGGAG 481 BONTA_X52066_538_552_F TATGGCTCTAC 239 BONTA_X52066_647_660_R TGTTACTGCTGGA 1346 TCAA T 482 BONTA_X5206_538_552P_F TA*TpGGC*Tp 143 BONTA_X52066_647_660P_R TG*Tp*TpA*Cp* 1146 *Cp*TpA*Cp* TpG*Cp*TpGGAT Tp*CpAA 483 BONTA_X5206_701_720_F GAATAGCAATT 94 BONTA_X5206_759_775_R TTACTTCTAACCC 1367 AATCCAAAT ACTC 484 BONTA_X52066_701_720P_F GAA*TpAG*Cp 91 BONTA_X52066_759_775P_R TTA*Cp*Tp*Tp* 1359 AA*Tp*TpAA* Cp*TpAA*Cp*Cp Tp*Cp*CpAAAT *CpA*Cp*TpC 485 BONTA_X5206_450_473_F TCTAGTAATAA 393 BONTA_X5206_517_539_R TAACCATTTCGCG 859 TAGGACCCTCA TAAGATTCAA GC 486 BONTA_X52066_450_473P_F T*Cp*TpAGTA 142 BONTA_X5206_517_539P_R TAACCA*Tp*Tp* 857 ATAATAGGA*C Tp*CpGCGTAAGA pCp*Cp*Tp* *Tp*Tp*CpAA C 487 BONTA_X52066_591_620_F TGAGTCACTTG 463 BONTA_X52066_644_671_R TCATGTGCTAATG 992 AAGTTGATACA TTACTGCTGGATC AATCCTCT TG 608 SSPE_BA_156_168P_F TGGTpGCpTpA 616 SSPE_BA_243_255P_R TGCpAGCpTGATp 1241 GCpATT TpGT 609 SSPE_BA_75_89P_F TACpAGAGTpT 192 SSPE_BA_163_177P_R TGTGCTpTpTpGA 1338 pTpGCpGAC ATpGCpT 610 SSPE_BA_150_168P_F TGCTTCTGGTp 533 SSPE_BA_243_264P_R TGATTGTTTTGCp 1191 GCpTpAGCpAT AGCpTGATpTpGT T 611 SSPE_BA_72_89P_F TGGTACpAGAG 602 SSPE_BA_163_182P_R TCATTTGTGCTpT 995 TpTpTpGCpGA pTpGAATpGCpT C 612 SSPE_BA_114_137P_F TCAAGCAAACG 255 SSPE_BA_196_222P_R TTGCACGTCpCpG 1401 CACAATpCpAG TTTCAGTTGCAAA AAGC TTC 699 SSPE_BA_123_153_F TGCACAATCAG 488 SSPE_BA_202_231_R TTTCACAGCATGC 1431 AAGCTAAGAAA ACGTCTGTTTCAG GCGCAAGCT TTGC 700 SSPE_BA_156_168_F TGGTGCTAGCA 612 SSPE_BA_243_255_R TGCAGCTGATTGT 1202 TT 701 SSPE_BA_75_89_F TACAGAGTTTG 179 SSPE_BA_163_177_R TGTGCTTTGAATG 1338 CGAC CT 702 SSPE_BA_150_168_F TGCTTTCTGGT 533 SSPE_BA_243_264_R TGATTGTTTTGCA 1190 GCTAGCATT GCTGATTGT 703 SSPE_BA_72_89_F TGGTACAGAGT 600 SSPE_BA_163_182_R TCATTTGTGCTTT 995 TTGCGAC GAATGCT 704 SSPE_BA_146_168_F TGCAAGCTTCT 484 SSPE_BA_242_267_R TTGTGATTGTTTT 1421 GGTGCTAGCAT GCAGCTGATTGTG T 705 SSPE_BA_63_89_F TGCTAGTTATG 518 SSPE_BA_163_191_R TCATAACTAGCAT 986 GTACAGAGTTT TTGTGCTTTGAAT GCGAC GCT 706 SSPE_BA_114_137_F TCAAGCAAACG 255 SSPE_BA_196_222_R TTGCACGTCTGTT 1402 CACAATCAGAA TCAGTTGCAAAT GC C 770 PLA_AF053945_7377_7402_F TGACATCCGGC 442 PLA_AF053945_7434_7462_R TCTAAATTCCGCA 1313 TCACGTTATTA AAGACTTTGGCAT TGGT TA 771 PLA_AF053945_7382_7404_F TCCGGCTCACG 327 PLA_AF053945_7482_7502_R TGGTCTGAGTACC 1304 TTATTATGGTA TCCTTTGC C 772 PLA_AF053945_7481_7503_F TGCAAAGGAGG 481 PLA_AF053945_7539_7562_R TATTGGAAATACC 943 TACTCAGACCA GGCAGCATCTC T 773 PLA_AF053945_7186_7211_F TTATACCGGAA 657 PLA_AF053945_7257_7280_R TAATGCGATACTG 879 ACTTCCCGAAA GCCTGCAAGTC GGAG 774 CAF1_AF053947_33407_33430_F TCAGTTCCGTT 292 CAF1_AF053947_33494_33514_R TGCGGGCTGGTTC 1235 ATCGCCATTGC AACAAGAG AT 775 CAF1_AF053947_33515_33541_F TCACTCTTACA 270 CAF1_AF053947_33595_33621_R TCCTGTTTTATAG 1053 TATAAGGAAGG CCGCCAAGAGTAA CGCTC G 776 CAF1_AF053947_33435_33457_F TGGAACTATTG 542 CAF1_AF053947_33499_33517_R TGATGCGGGCTGG 1183 CAACTGCTAAT TTCAAC G 777 CAF1_AF053947_33687_33716_F TCAGGATGGAA 286 CAF1_AF053947_33755_33782_R TCAAGGTTCTCAC 962 ATAACCACCAA CGTTTACCTTAGG TTCACTAC AG 778 INV_U22457_515_539_F TGGCTCCTTGG 573 INV_U22457_571_598_R TGTTAAGTGTGTT 1343 TATGACTCTGC GCGGCTGTCTTTA TTC TT 779 INV_U22457_699_724_F TGCTGAGGCCT 525 INV_U22457_753_776_R TCACGCGACGAGT 976 GGACCGATTAT GCCATCCATTG TTAC 780 INV_U22457_834_858_F TTATTTACCTG 664 INV_U22457_942_966_R TGACCCAAAGCTG 1154 CACTCCCACAA AAAGCTTTACTG CTG 781 INV_U22457_1558_1581_F TGGTAACAGAG 597 INV_U22457_1619_1643_R TTGCGTTGCAGAT 1408 CCTTATAGGCG TATCTTTACCAA CA 782 LL_NC003143_2366996_(—) TGTACCCGCTAA 627 LL_NC003143_2367073_2367097_R TCTCATCCCGATA 1123 2367019_F AGCACTACCAT TTACCGCCATGA CC 783 LL_NC003143_2367172_(—) TGGACGGCATC 550 LL_NC003143_2367249_23672 TGGCAACAGCTCA 1272 2367194_F ACGATTCTCTA ACACCTTTGG C 874 RPLB_EC_649_679_F TGICCIACIGT 620 RPLB_EC_739_762_TMOD_R TTCCAAGTGCTGG 1380 IIGIGGTTCTG TTTACCCCATGG TAATGAACC 875 RPLB_EC_642_679P_F TpCpCpTpTpG 646 RPLB_EC_739_762_TMOD_R TTCCAAGTGCTGG 1380 ITpGICCIACI TTTACCCCATGG GTIIGIGGTTC TGTAATGAACC 876 MECIA_Y14051_3315_3341_F TTACACATATC 653 MECIA_Y14051_3367_3393_R TGTGATATGGAGG 1333 GTGAGCAATGA TGTAGAAGGTGTT ACTGA A 877 MECA_Y14051_3774_3802_F TAAAACAAACT 144 MECA_Y14051_3828_3854_R TCCCAATCTAACT 1015 ACGGTAACATT TCCACATACCATC GATCGCA T 878 MECA_Y14051_3645_3670_F TGAAGTAGAAA 434 MECA_Y14051_3690_3719_R TGATCCTGAATGT 1181 TGACTGAACGT TTATATCTTTAAC CCGA GCCT 879 MECA_Y14051_4507_4530_F TCAGGTACTGC 288 MECA_Y14051_4555_4581_R TGGATAGACGTCA 1269 TATCCACCCTC TATGAAGGTGTGC AA T 880 MECA_Y14051_4510_4530_F TGTACTGCTAT 626 MECA_Y14051_4586_4610_R TATTCTTCGTTAC 939 CCACCCTCAA TCATGCCATACA 881 MECA_Y14051_4669_4698_F TCACCAGGTTC 262 MECA_Y14051_4765_4793_R TAACCACCCCAAG 858 AACTCAAAAAA ATTTATCTTTTG ATATTAACA CCA 882 MECA_Y14051_4520_4530P_F TCpCpACpCpC 389 MECA_Y14051_4590_4600P_R TpACpTpCpATpG 1357 pTpCpAA CpCpA 883 MECA_Y14051_4520_4530P_F TCpCpACpCpC 389 MECA_Y14051_4600_4610P_R TpATpTpCpTpTp 1358 pTpCpAA CpGTpT 902 TRPE_AY094355_1467_1491_F ATGTCGATTGC 36 TRPE_AY094355_1569_1592_R TGCGCGAGCTTT 1231 AATCCGTACTT TATTTGGGTTTC GTG 903 TRPE_AY094355_1445_1471_F TGGATGGCATG 557 TRPE_AY094355_1551_1580_R TATTTGGGTTTCA 944 GTGAAATGGAT TTCCACTCAGATT ATGTC CT 904 TRPE_AY094355_1278_1303_F TCAAATGTACA 247 TRPE_AY094355_1392_1418_R TCCTCTTTTCACA 1048 AGGTGAAGTGC GGCTCTACTTCAT GTGA C 905 TRPE_AY094355_1064_1086_F TCGACCTTTGG 357 TRPE_AY094355_1171_1196_R TACATCGTTTCGC 885 CAGGAACTAGA CCAAGATCAATCA C 906 TRPE_AY094355_666_688_F GTGCATGCGGA 135 TRPE_AY094355_769_791_R TTCAAAATGCGGA 1372 TACAGAGCAGA GGCGTATGTG 907 TRPE_AY094355_757_776_F TGCAAGCGCGA 483 TRPE_AY094355_864_883_R TGCCCAGGTACAA 1218 CCACATACG CCTGCAT 908 RECA_AF251469_43_68_F TGGTACATGTG 601 RECA_AF251469_140_163_R TTCAAGTGCTTGC 1375 CCTTCATTGAT TCACCATTGTC GCTG 909 RECA_AF251469_169_190_F TGACATGCTTG 446 RECA_AF251469_277_300_R TGGCTCATAAGAC 1280 TCCGTTCAGGC GCGCTTGTAGA 910 PARC_X95819_87_110_F TGGTGACTCGG 609 PARC_X95819_201_222_R TTCGGTATAACGC 1387 CATGTTATGAA ATCGCAGCA GC 911 PARC_X95819_87_110_F TGGTGACTCGG 609 PARC_X95819_192_219_R GGTATAACGCATG 836 CATGTTATGAA GCAGCAAAAGATT GC TA 912 PARC_X95819_123_147_F GGCTCAGCCAT 120 PARC_X95819_232_260_R TCGCTCAGCAATA 1081 TTAGTTACCGC ATTCACTATAAGC TAT CGA 913 PARC_X95819_43_63_F TCAGCGCGTAC 277 PARC_X95819_143_170_R TTCCCCTGACCTT 1383 AGTGGGTGAT CGATTAAAGGATA GC 914 OMPA_AY485227_272_301_F TTACTCCATTA 655 OMPA_AY485227_364_388_R GAGCTGCGCCAAC 812 TTGCTTGGTTA GAATAAATCGTC CACTTTCC 915 OMPA_AY485227_379_401_F TGCGCAGCTCT 509 OMPA_AY485227_492_519_R TGCCGTAACATAG 1223 TGGTATCGAGT AAGTTACCGTTGA T T 916 OMPA_AY485227_311_335_F TACACAACAAT 178 OMPA_AY485227_424_453_R TACGTCGCCTTA 901 GGCGGTAAAGA ACTTGGTTATATT TGG CAGC 917 OMPA_AY485227_415_441_F TGCCTCGAAGC 506 OMPA_AY485227_514_546_R TCGGGCGTAGTTT 1092 TGAATATAACC TTAGTAATTAAAT AAGTT CAGAAGT 918 OMPA_AY485227_494_520_F TCAACGGTAAC 252 OMPA_AY485227_569_596_R TCGTCGTATTTAT 1108 TTCTATGTTAC AGTGACCAGCACC TTCTG TA 919 OMPA_AY485227_551_577_F TCAAGCCGTAC 257 OMPA_AY485227_658_680_R TTTAAGCGCCAGA 1425 GTATTATTAGG AAGCACCAAC TGCTG 920 OMPA_AY485227_555_581_F TCCGTACGTAT 328 OMPA_AY485227_635_662_R TCAACACCAGCGT 954 TATTAGGTGCT TACCTAAAGTACC GGTCA TT 921 OMPA_AY485227_556_583_F TCGTACGTATT 379 OMPA_Y485227_659_683_R TCGTTTAAGCGCC 1114 ATTAGGTGCTG AGAAAGCACCAA GTCACT 922 OMPA_AY485227_657_679_F TGTTGGTGCTT 645 OMPA_AY485227_139_765_R TAAGCCAGCAAGA 871 TCTGGCGCTTA GCTGTATAGTTCC A A 923 OMPA_AY485227_660_683_F TGGTGCTTTCT 613 OMPA_AY485227_786_807_R TACAGGAGCAGCA 884 GGCGCTTAAAC GGCTTCAAG GA 924 GYRA_AF100557_4_23_F TCTGCCCGTGT 402 GYRA_AF100557_119_142_R TCGAACCGAAGTT 1063 CGTTGGTGA ACCCTGACCAT 925 GYRA_AF100557_70_94_F TCCATTGTTCG 316 GYRA_AF100557_178_201_R TGCCAGCTTAGTC 1211 TATGGCTCAAG ATACGGACTTC 926 GYRB_AB008700_19_40_F TCAGGTGGCT 289 GYRB_AB008700_111_140_R TATTGCGGATCAC 941 TACACGGCGT CATGATGATATTC AG TTGC 927 GYRB_AB008700_265_292_F TCTTTCTTGAA 420 GYRB_AB008700_369_395_R TCGTTGAGATGGT 1113 TGCTGGTGTAC TTTTACCTTCGT GTATCG TG 928 GYRB_AB008700_368_394_F TCAACGAAGGT 251 GYRB_A3008700_466_494_R TTTGTGAAACAGC 1440 AAAAACCATCT GAACATTTTCTTG CAACG GTA 929 GYRB_AB008700_477_504_F TGTTCGCTGTT 641 GYRB_AB008700_611_632_R TCACGCGCATCAT 977 TCACAAACAAC CACCAGTCA ATTCCA 930 GYRB_AB008700_760_787_F TACTTACTTGA 198 GYRB_AB008700_862_888_R ACCTGCAATATCT 729 GAATCCACAAG AATGCACTCTTAC CTGCAA G 931 WAAA_Z96925_2_29_F TCTTGCTCTTT 416 WAAA_Z96925_115_138_R CAAGCGGTTTGCC 758 CGTGAGTTCAG TCAAATAGTCA TAAATG 932 WAAA_Z96925_286_311_F TCGATCTGGTT 360 WAAA_Z96925_394_412_R TGGCACGAGCCTG 1274 TCATGCGTTT ACCTGT 939 RPOB_EC_3798_3821_F TGGGCAGCGTT 581 RPOB_EC_9862_3889_R TGTCCGACTTGAC 1326 TCGGCGAAATG GGTCAGCATTTCC GA TG 940 RPOB_EC_3798_3821_F TGGGCAGCGTT 581 RPOB_EC_3862_3899_2_R TGTCCGACTTGAC 1327 TCGGCGAAATG GGTTAGCATTTCC GA TG 941 TUFB_EC_275_299_F TGATCACTGGT 468 TUFB_EC_337_362_R TGGATGTGCTCAC 1271 GCTGCTCAGAT GAGTCTGTGGCAT GGA 942 TUFB_EC_251_278_F TGCACGCCGAC 493 TUFB_EC_337360_R TATGTGCTCACGA 937 TATGTTAAGAA GTTTGCGGCAT CATGAT 949 GYRE_AB008700_760_787_F TACTTACTTGA 198 GYRB_AB008700_862_888_2_R TCCTGCAATATCT 1050 GAATCCACAAG AATGCACTCTTAC CTGCAA G 958 RPOC_EC_2223_2243_F TGGTATGCGTG 605 RPOC_EC_2329_2352_R TGCTAGACCTTTA 1243 GTCTGATGGC CGTGCACCGTG 959 RPOC_EC_918_938_F TCTGGATAACG 404 RPOC_EC_1009_1031_R TCCAGCAGGTTCT 1004 GTCGTCGCGG GACGGAAACG 960 RPOC_EC_2334_2357_F TGCTCGTAAGG 523 RPOC_EC_2380_2403_R TACTAGACGACGG 905 GTCTGGCGGAT GTCAGGTAACC AC 961 RPOC_EC_917_938_F TATTGGACAAC 242 RPOC_EC_1009_1034_R TTACCGAGCAGGT 1362 GGTCGTCGCGG TCTGACGGAAACG 962 RPOB_E2005_2027_F TCGTTCCTGGA 387 RPOB_EC_2041_2064_R TTGACGTTGCATG 1399 ACACGATGACG TTCGAGCCCAT C 963 RPOB_EC_1527_1549_F TCAGCTGTCGC 282 RPOB_EC_1630_1649_R TCGTCGCGGACTT 1104 AGTTCATGGAC CGAAGCC C 964 INFB_EC_1347_1367_F TGCGTTTACCG 515 INFB_EC_1414_1432_R TCGGCATCACGCC 1090 CAATGCGTGC GTCGTC 965 VALS_EC_1128_1151_F TATGCTGACCG 237 VALS_EC_1231_1257_R TTCGCGCATCCAG 1384 ACCAGTGGTAC GAGAAGTACATGT GT T 978 RPOC_EC_2145_2175_F TCAGGAGTCGT 285 RPOC_EC_2228_2247_R TTACGCCATCAGG 1363 TCAACTCGATC CCACGCA TACATGATG 1045 CJST_CJ_1668_1700_F TGCTCGAGTGA 522 CJST_CJ_1774_1799_R TGAGCGTGTGGAA 1170 TTGACTTTGCT AAGGACTTGGATG AAATTTAGAGA 1046 CJST_CJ_2171_2197_F TCGTTTGGTGG 388 CJST_CJ_2283_2313_R TCTCTTTCAAAGC 1126 TGGTAGATGAA ACCATTGCTCATT AAAGG ATAGT 1047 CJST_CJ_584_616_F TCCAGGACAAA 315 CJST_CJ_663_692_R TTCATTTTCTGGT 1379 TGTATGAAAAA CCAAAGTAAGCAG TGTCCAAGAAG TATC 1048 CJST_CJ_360_394_F TCCTGTTATCC 346 CJST_CJ_442_476_R TCAACTGGTTCAA 955 CTGAAGTAGTT AAACATTAAGTTG AATCAAGTTTG TAATTGTCC TT 1049 CJST_CJ_2636_2668_F TGCCTAGAAGA 504 CJST_CJ_2753_2777_R TTGCTGCCATAGC 1409 TCTTAAAAATT AAAGCCTACAGC TCCGCCAACTT 1050 CJST_CJ_1290_1320_F TGGCTTATCCA 575 CJST_CJ_1406_1433_R TTTGCTCATGATC 1437 AATTTAGATCG TGCATGAAGCATA TGGTTTTAC AA 1051 CJST_CJ_3267_3293_F TTTGATTTTAC 707 CJST_CJ_3356_3385_R TCAAAGAACCCGC 951 GCCGTCCTCCA ACCTAATTCATCA GGTCG TTTA 1052 CJST_CJ_5_39_F TAGGCGAAGAT 222 CJST_CJ_104_137_R TCCCTTATTTTTC 1029 ATACAAAGAGT TTTCTACTACCTT ATTAGAAGCT CGGATAAT AGA 1053 CJST_CJ_1080_1110_F TTGAGGGTATG 681 CJST_CJ_1166_1198_R TCCCTCATGTTT 1022 CACCGTCTTT AAATGATCAGGAT TTGATTCTTT AAAAAGC 1054 CJST_CJ_2060_2090_F TCCCGGACTTA 323 CJST_CJ_2148_2174_R TCGATCCGCATCA 1068 ATATCAATGAA CCATCAAAAGCAA AATTGTGGA A 1055 CJST_CJ_2869_2895_F TGAAGCTTGTT 432 CJST_CJ_2979_3007_R TCCTCCTTGTGCC 1045 CTTTAGCAGGA TCAAAACGCATTT CTTCA TTA 1056 CJST_CJ_1880_1910_F TCCCAATTAAT 317 CJST_CJ_1981_2011_R TGGTTCTTACTTG 1309 TCTGCCATTTT CTTTGCATAAACT TCCAGGTAT TTCCA 1057 CJST_CJ_2185_2212_F TAGATGAAAAG 208 CJST_CJ_2283_2316_R TGAATTCTTTCAA 1152 GGCGAAGTGGC AGCACCATTGCTC TAATGG ATTATAGT 1058 CJST_CJ_1643_1670_F TTATCGTTTGT 660 CJST_CJ_1724_1752_R TGCAATGTGTGCT 1198 GGAGCTAGTGC ATGTCAGCAAA TTATGC AAGAT 1059 CJST_CJ_2165_2194_F TGCGGATCGTT 511 CJST_CJ_2247_2278_R TCCACACTGGATT 1002 TGGTGGTTGTA GTAATTTACCTTG GATGAAAA TTCTTT 1060 CJST_CJ_599_632_F TGAAAAATGTC 424 CJST_CJ_711_743_R TCCCGAACAATGA 1024 CAAGAAGCATA GTTGTATCAACTA GCAAAAAAAGC TTTTTAC A 1061 CJST_CJ_360_393_F TCCTGTTATCC 345 CJST_CJ_443_477_R TACAACTGGTTCA 882 CTGAAGTAGTT AAAACATTAAGCT AATCAAGTTTG GTAATTGTC T 1062 CJST_CJ_2678_2703_F TCCCCAGGACA 321 CJST_CJ_2760_2787_R TGTGCTTTTTTTG 1339 CCCTGAAATTT CTGCCATAGCAAA CAAC GC 1063 CJST_CJ_1268_1299_F AGTTATAAACA 29 CJST_CJ_1349_1379_R TCGGTTTAAGCTC 1096 CGGCTTTCCTA TACATGATCGTAA TGGCTTATCC GGATA 1064 CJST_CJ_1680_1713_F TGATTTTGCTA 479 CJST_CJ_1795_1822_R TATGTGTAGTTGA 938 AATTTAGAGAA GCTTACTACATGA ATTGCGGATGA GC A 1065 CJST_CJ_2857_2887_F TGGCATTTCTT 565 CJST_CJ_2965_2998_R TGCTTCAAAACGC 1253 ATGAAGCTTGT ATTTTTACATTTT TCTTTAGCA CGTTAAAG 1070 RNASEP_BKM_580_599_F TGCGGGTAGGG 512 RNASEP_BKM_665_686_R TCCGATAAGCCGG 1034 AGCTTGAGC ATTCTGTGC 1071 RNASEP_BKM_616_637_F TCCTAGAGGAA 333 RNASEP_BKM_665_687_R TGCCGATAAGCCC 1222 TGGCTGCCACG GGATTCTGTGC 1072 RNASEP_BDP_574_592_F TGGCACGGCCA 561 RNASEP_BDP_616_635_R TCGTTTCACCCTG 1115 TCTCCGTG TCATGCCG 1073 23S_BRM_1110_1129_F TGCGCGGAAGA 510 23S_BRM_1176_1201_R TCGCAGGCTTACA 1074 TGTAACGGG GAACGCTCTCCTA 1074 23S_BRM_515_536_F TGCATACAAAC 496 23S_BRM_616_635_R TCGGACTCGCTTT 1088 AGTCGGAGCCT CGCTACG 1075 RNASEP_CLB_459_487_F TAAGGATAGTG 162 RNASEP_CLB_498_526_R TGCTCTTACCTCA 1247 CAACAGAGATA CCGTTCCACCCTT TACCGCC ACC 1076 RNASEP_CLB_459_487_F TAAGGATAGTG 162 RNASEP_CLB_498_522_R TTTACCTCGCCTT 1426 CAACAGAGATA TCCACCCTTACC TACCGCC 1077 ICD_CXB_93_120_F TCCTGACCGAC 343 ICD_CXB_172_194_R TAGGATTTTTCCA 921 CCATTATTCCC CGGCGGCATC TTTATC 1078 ICD_CXB_92_120_F TTCCTGACCGA 671 ICD_CXB_172_194_R TAGGATTTTTCCA 921 CCCATTATTCC CGGCGGCATC CTTTATC 1079 ICD_CXB_176_198_F TCGCCGTGGAA 369 ICD_CXB_224_247_R TAGCCTTTTCTCC 916 AAATCCTACGC GGCGTAGATCT T 1080 IS1111A_NC002971_6866_(—) TCAGTATGTAT 290 IS1111A_NC002971_6928_6954_R TAAACGTCCGATA 848 6891_F CCACCGTAGCC CCAATGGTTCGCT GTC C 1081 IS1111A_NC002971_7456_(—) TGGGTGACATT 594 IS1111A_NC002971_7529_7554_R TCAACAACACCTC 952 7483_F CATCAATTTCA CTTATTCCCACTC TCGTTC 1082 RNASEP_RKP_419_448_F TGGTAAGAGCG 599 RNASEP_RKP_542_565_R TCAAGCGATCTAC 957 TGGTAACA CCGCATTACAA 1083 RNASEP_RKP_422_443_F TAAGAGCGCAC 159 RNASEP_RKP_542_565_R TCAAGCGATCTAC 957 CGGTAAGTTGG CCGCATTACAA 1084 RNASEP_RKP_466_491_F TCCACCAAGAG 310 RNASEP_RKP_542_565_R TCAAGCGATCTAC 957 CAAGATCAAAT CCGCATTACAA AGGC 1085 RNASEP_RKP_264_287_F TCTAAATGGTC 391 RNASEP_RKP_295_321_R TCTATAGAGTCCG 1119 GTGCAGTTGCG GACTTTCCTCGTG TG A 1086 RNASEP_RKP_426_448_F TGCATACCGGT 497 RNASEP_RKP_542_565_R TCAAGCGATCTAC 957 AAGTTGGCAAC CCGCATTACAA A 1087 OMPB_RKP_860_890_F TTACAGGAAGT 654 OMPB_RKP_972_996_R TCCTGCAGCTCTA 1051 TTAGGTGGTAA CCTGCTCCATTA TCTAAAAGG 1088 OMPB_RKP_1192_1221_F TCTACTGATTT 392 OMPB_RKP_1288_1315_R TAGCAgCAAAGT 910 TGGTAATCTTG TATCACACCTGCA CAGCACAG GT 1089 OMPB_RKP_3417_3440_F TGCAAGTGGTA 485 OMPB_RKP_3520_3550_R TGGTTGTAGTTCC 1310 CTTCAACATGG TGTAGTTGTTGCA GG TTAAC 1090 GLTA_RKP_1043_1072_F TGGGACTTGAA 576 GLTA_RKP_1138_1162_R TGAACATTTGCGA 1147 GCTATCGCTCT CGGTATACCCAT TAAAGATG 1091 GLTA_RKP_400_428_F TCTTCTCATCC 413 GLTA_RKP_499_529_R TGGTGGGTATCTT 1305 TATGGCTATTA AGCAATCATTCTA TGCTTGC ATAGC 1092 GLTA_RKP_1023_1055_F TCCGTTCTTA 330 GLTA_RKP_1129_1156_R TTGGCGACGGTAT 1415 AAATAGCAATA ACCCATAGCTTTA GAACTTGAAGC TA 1093 GLTA_RKP_1043_1072_2_F TGGAGCTTGAA 553 GLTA_RKP_1138_1162_R TGAACATTGCGA 1147 GCTATCGCTCT CGGTATACCCAT AAAGATG 1094 GLTA_RKP_1043_1072_3_F TGGAACTTGAA 543 GLTA_RKP_1138_1164_R TGTGAACATTTGC 1330 GCTCTCGCTCT GACGGTATACCCA TAAAGATG T 1095 GLTA_RKP_400_428_F TCTTCTCATCC 413 GLTA_RKP_505_534_R TGCGATGGTAGGT 1230 TATGGCTATTA ATCTTAGCAATCA TGCTTGC TTCT 1096 CTXA_VBC_117_142_F TCTTATGCCAA 410 CTXA_VBC_194_218_R TGCCTAACAAATC 1226 GAGGACAGAGT CCGTCTGAGTTC GAGT 1097 CTXA_VBC_351_377_F TGTATTAGGGG 630 CTXA_VBC_441_466_R TGTCATCAAGCAC 1324 CATACAGTCCT CCAAAATGAACT CATCC 1098 RNASEP_VBC_331_349_F TCCGCGGAGTT 325 RNASEP_VBC_388_414_R TGACTTTCCTCCC 1163 GACTGGGT CCTTATCAGTCTC C 1099 TOXR_VBC_135_158_F TCGATTAGGCA 362 TOXR_VBC_221_246_R TTCAAAACCTTGC 1370 GCAACGAAAGC TCTCGCCAAACAA CG 1100 ASD_FRT_1_29_F TTGCTTAAAGT 690 ASD_FRT_86_116_R TGAGATGTCGAAA 1164 TGGTTTTATTG AAAACGTTGGCAA GTTGGCG AATAC 1101 ASD_FRT_43_76_F TCAGTTTTAAT 295 ASD_FRT_129_156_R TCCATATTGTTGC 1009 GTCTCGTATGA ATAAAACCTGTTG TCGAATCAAAA GC G 1102 GALE_FRT_168_199_F TTATCAGCTAG 658 GALE_FRT_241_269_R TCACCTACAGCTT 973 ACCTTTTAGGT TAAAGCCAGCAAA AAAGCTAAGC ATG 1103 GALE_FRT_834_865_F TCAAAAAGCCC 245 GALE_FRT_901_925_R TAGCCTTGGCAAC 915 TAGGTAAAGAG ATCAGCAAAACT ATTCCATATC 1104 GALE_FRT_308_339_F TCCAAGGTACA 306 GALE_FRT_390_422_R TCTTCTGTAAAGG 1136 CTAAACTTACT GTGGTTTATTATT TGAGCTAATG CATCCCA 1105 IPAH_SGF_258_277_F TGAGGACCGTG 458 IPAH_SGF_301_327_R TCCTTCTGATGCC 1055 TCGCGCTCA TGATGGACCAGGA G 1106 IPAH_SGF_113_134_F TCCTTGACCGC 350 IPAH_SGF_172_191_R TTTTCCAGCCATG 1441 CTTTCCGATAC CAGCGAC 1107 IPAH_SGF_462_486_F TCAGACCATGC 271 IPAH_SGF_522_540_R TGTCACTCCCGAC 1322 TCGCAGAGAAA ACGCCA CTT 1111 RNASEP_BRM_461_488_F TAAACCCCATC 147 RNASEP_BRM_542_561_R TGCCTCGCGCAAC 1227 GGGAGCAAGAC CTACCCG CGAATA 1112 RNASEP_BRM_325_347_F TACCCCAGGGA 185 RNASEP_BRM_402_428_R TCTCTTACCCCAC 1125 AAGTGCCACAG CCTTTCACCCTTA A C 1128 HUPB_CJ_113_134_F TAGTTGCTCAA 230 HUPB_CJ_157_188_R TCCCTAATAGTAG 1028 ACAGCTGGGCT AAATAACTGCATC AGTAGC 1129 HUPB_CJ_76_102_F TCCCGGAGCTT 324 HUPB_CJ_157_188_R TCCCTAATAGTAG 1028 TTATGACTAAA AAATAACTGCATC GCAGAT AGTAGC 1130 HUPB_CJ_102_F TCCCGGAGCTT 324 HUPB_CJ_114_135_R TAGCCCAGCTGTT 913 TTATGACTAAA TGAGCAACT GCAGAT 1151 AB_MLST-11- TGAGATTGCTG 454 AB_MLST-11- TTGTACATTTGAA 1418 OIF007_62_91_F AACATTTAATG OIF007_169_203_R ACAATATGCATGA CTGATTGA CATGTGAAT 1152 AB_MLST-11- TATTGTTTCAA 243 AB_MLST-11- TCACAGGTTCTAC 969 OIF007_185_214_F ATGTACAAGGT OIF007_291_324_R TTCATCAATAATT GAAGTGCG TCCATTGC 1153 AB_MLST-11- TGGAACGTTAT 541 AB_MLST-11- TTGCAATCGACAT 1400 OIF007_260_289_F CAGGTGCCCCA OIF007_364_393_R ATCCATTTCACCA AAATTCG TGCC 1154 AB_MLST-11- TGAAGTGCGTG 436 AB_MLST-11- TCCGCCAAAAACT 1036 OIF007_206_239_F ATGATATCGAT OIF007_318_344_R CCCCTTTTCACAG GCACTTGATGT G A 1155 AB_MLST-11- TCGGTTTAGTA 378 AB_MLST-11- TTCTGCTTGAGGA 1392 OIF007_522_552_F AAAGAACGTAT OIF007_587_610_R ATAGTGCGTGG TGCTCAACC 1156 AB_MLST-11- TCAACCTGACT 250 AB_MLST-11- TACGTTCTACGAT 902 OIF007_547_571_F GCGTGAATGGT OIF007_656_686_R TTCTTCATCAGGT TGT ACATC 1157 AB_MLST-11- TCAAGCAGAAG 256 AB_MLST-11- TACAACGTGATAA 881 OIF007_601_627_F CTTTGGAAGAA OIF007_710_736_R ACACGACCAGAAG GAAGG C 1158 AB_MLST-11- TCGTGCCCGCA 384 AB_MLST-11- TAATGCCGGGTAG 878 OIF007_1202_1225_F ATTGCATAAA OIF007_1266_1296_R TGCAATCCATTCT GC TCTAG 1159 AB_MLST-11- TCGTCCCGCA 384 AB_MLST-11- TGCACCTGCGGTC 1199 OIG007_1202_1225_F ATTTGCATAAA OIF007_1299_1316_R GAGCG GC 1160 AB_MLST-11- TTGTAGCACAG 694 AB_MLST-11- TGCCATCCATAAT 1215 OIF007_1234_1264_F TCCTGAAAC OIF007_1335_1362_R CACGCCATACTGA CG 1161 AB_MLST-11- TAGGTTTACGT 225 AB_MLST-11- TGCCAGTTTCCAC 1212 OIF007_1327_1356_F GATTATGG OIF007_1422_1448_R ATTTCACGTTCGT G 1162 AB_MLST-11- TCGTGATTATG 383 AB_MLST-11- TCGCTTGAGTGTA 1083 OIF007_1345_1369_F AA OIF007_1470_1494_R GTCATGATTGCG 1163 AB_MLST-11- TTATGGATGGC 662 AB_MLST-11- TCGCTTGAGTGTA 1083 OIF007_1351_1375_F GT OIF007_1470_1494_R GTCATGATTGCG 1164 AB_MLST-11- TCTTTGCCATT 422 AB_MLST-11- TCGCTTGAGTGTA 1083 OIF007_1387_1412_F GAAGATGACTT OIF007_1470_1494_R GTCATAGATTGCG AAGC 1165 AB_MLST-11- TACTAGCGGTA 194 AB_MLST-11- TGAGTCGGGTTCA 1173 OIF007_1542_1569_F AGCTTAAACAA OIF007_1656_1680_R CTTACCTGGCA GATTGC 1166 AB_MLST-11- TTGCCAATGAT 684 AB_MLST-11- TGAGTCGGGTTCA 1173 OIF007_1566_1593_F ATTCGTTGGTT OIF007_1656_1680_R CTTTACCTGGCA AGCAAG 1167 AB_MLST-11- TCGGCGAAATC 375 AB_MLST-11- TACCGGAAGCACC 890 OIF007_1611_1638_F CGTATTCCTGA OIF007_1731_1757_R AGCGACATTAATA AAATGA G 1168 AB_MLST-11- TACCACTATTA 182 AB_MLST-11- TGCAACTGAATAG 1195 OIF007_1726_1752_F ATGTCGCTGGT OIF007_1790_1821_R ATTGCAGTAAGTT GCTTC ATAAGC 1169 AB_MLST-11- TTATAACTTAC 656 AB_MLST-11- TGAATTATGCAAG 1151 OIF007_1792_1826_F TGCAATCTATT OIF007_1876_1909_R AAGTGATCAATTT CAGTTGCTG TCTCACGA GTG 1170 AB_MLST-11- TTATAACTTAC 656 AB_MLST-11- TGCCGTAACTAAC 1224 OIF007_1792_1826_F TGCAATCTATT OIF007_1895_1927_R ATAAGAGAATTAT CAGTTGCTTGG GCAAGAA TG 1171 AB_MLST-11- TGGTTATGTAC 618 AB_MLST-11- TGACGGCATCGA 1157 OIF007_1970_2002_F CAAATACTTTG OIF007_2097_2118_R ACCACCGTC TCTGAAGAGG 1172 RNASEP_BRM_461_488_F TAAACCCCATC 147 RNASEP_BRM_542_561_2_R TGCCTCGTGCAAC 1228 GGGAGCAAGAC CCACCCG CGAATA 2000 CTXB_NC002505_46_70_F TCAGCGTATGC 278 CTSB_NC002505_132_162_R TCCGGCTAGAGAT 1039 ACATGGAACTC TCTGTATACGAC CTC AATATC 2001 FUR_NC002505_87_113_F TGAGTGCCAAC 465 FUR_NC002505_205_228_R TCCGCCTTCAAAA 1037 ATATCAGTGCT TGGTGGCGAGT GAAGA 2002 FUR_NC002505_87_113_F TGAGTGCCAAC 465 FUR_NC002505_178_205_R TCACGATACCTGC 974 ATATCAGTGCT ATCATCAAATTG GAAGA GTT 2003 GAPA_NC002505_533_560_F TCGACAACACC 356 GAPA_NC002505_646_671_R TCAGAATCGATGC 980 ATTATCTATGG CAAATGCGTCATC 2004 GAPA_NC002505_505_19_721_F TCAATGAACGA 259 GAPA_NC002505_769_798_R TCCTCTATGCAAC 1046 CCAACAAGTGA TTAGTATCAACA TTGATG GAAT 2005 GAPA_NC002505_753_782_F TGCTAGTCAAT 517 GAPA_NC002505_856_881_R TCCATCGCAGTCA 1011 CTATCATTCCG CGTTTACTGTTGG GTTGATAC 2006 GYRB_NC002505_2_32_F TGCCGGACAAT 501 GYRB_NC002505_109_134_R TCCACCACCTCAA 1003 TACGATTCATC AGACCATGTGGTG GAGTATTAA 2007 GYRB_NC002505_123_152_F TGAGGTGGTGG 460 GYRB_NC002505_199_225_R TCCGTCATCGCTG 1042 ATAACTCAATT ACAGAAACTGAGT GATGAAGC T 2008 GYRB_NC002505_768_794_F TATGCAGTGGA 236 GYRB_NC002505_832_860_R TGGAAACCGGCTA 1262 ACGATGGTTTC AGTGAGTACCACC CAAGA ATC 2009 GYRB_NC002505_837_860_F TGGTACTCACT 603 GYRB_NC002505_937_957_R TCCTTCACGCGCA 1054 TAGCGGGTTT TCATCACC CG 2010 GYRB_NC002505_934_956_F TCGGGTGATGA 377 GYRB_NC002505_982_1007_R TGGCTTGAGAATT 1283 TGCGCGTGAAG TAGGATCCGGCAC G 2011 GYRB_NC002505_1161_1190_F TAAAGCCCGTG 148 GYRB_NC002505_1255_1284_R TGAGTCACCCTCC 1172 AAATGACTCGT ACAATGTATAGTT CGTAAAGG CAGA 2012 OMPU_NC002505_275_110_F TACGCTGACGG 190 OMPU_NC002505_154_180_R TGCTTCAGCACGG 1254 AATCAACCAAA CCACCAACTTCTA GCGG G 2013 OMPU_NC002505_258_283_F TGACGGCCTAT 451 OMPU_NC002505_346_369_R TCCGAGACCAGCG 1033 ACGGTGTTGGT TAGGTGTAACG TTCT 2014 OMPU_NC002505_431_455_F TCACCGATATC 266 OMPU_NC002505_544_567_R TCGGTCAGCAAAA 1094 ATGGCTTACCA CGGTAGCTTGC CGG 2015 OMPU_NC002505_533_557_F TAGGCGTGAAA 223 OMPU_NC002505_625_651_R TAGAGAGTAGCCA 908 GCAAGCTACCG TCTTCACCGTTGT TTT C 2016 OMPU_NC002505_689_713_F TAGGTGCTGGT 224 OMPU_NC002505_725_751_R TGGGGTAAGACGC 1291 TACGCAGATCA GGCTAGCATGTAT AGA T 2017 OMPU_NC002505_727_747_F TACATGCTAGC 181 OMPU_NC002505_811_835_R TAGCAGCTAGCTC 911 CGCGTCTTAC GTAACCAGTGTA 2018 OMPU_NC002505_931_953_F TACTACTTCAA 193 OMPU_NC002505_1033_1053_R TTAGAAGTCGTAA 1368 GCCGAACTTCC CGTGGACC G 2019 OMPU_NC002505_927_953_F TACTTACTACT 197 OMPU_NC002505_1033_1054_R TGGTTAGAAGTCG 1307 TCAAGCCGAAC TAACGTGGACC TTCCG 2020 TCPA_NC002505_48_73_F TCACGATAAGA 269 TCPA_NC002505_148_170_R TTCTGCGAATCAA 1391 AAACCGGTCAA TCGCACGCTG GAGG 2021 TDH_NC004605_265_289_F TGGCTGACATC 574 TDH_NC004605_357_386_R TGTTGAAGCTGTA 1351 CTACATGACTG CTTGACCTGATTT TGA TACG 2022 VVHA_NC004460_772_802_F TCTTATTCCAA 412 VVHA_NC004460_862_886_R TACCAAAGCGTGC 887 CTTCAAACCGA ACGATAGTTGAG ACTATGACG 2023 23S_EC_2643_2667_F TGCCTGTTCTT 508 23S_EC_2746_2770_R TGGGTTTCGCGCT 1297 AGTACGAGAGG AGATGCTTTCA ACC 2024 16S_EC_713_732_TMOD_F TAGAACACCCG 202 16S_EC_789_811_R TGCGTGGACTAC 1240 ATGGCGAAGGC AGGGTATCTA 2025 16S_EC_784_806_F TGGATTAGAGA 560 16S_EC_880_897_TMOD_R TGGCCGTACTCCC 1278 CCCTGGTAGTC CAGGCG C 2026 16S_EC_959_981_F TGTCGATGCAA 634 16S_EC_1052_1074_R TACGAGCTGACGA 896 CGCGAAGAACC CAGCCATGCA T 2027 TUFB_EC_956_979_F TGCACACGCCG 489 TUFB_EC_1034_1058_2_R TGCATCACCATTT 1204 TTCTTCAACAA CCTTGTCCTTCG CT 2028 RPOC_EC_2146_2174_TMOD_F TCAGGAGTCGT 284 RPOC_EC_2227_2249_R TGCTAGGCCATCA 1244 TCAACTCGATC GGCCACGCAT TACATGAT 2029 RPOB_EC_1841_1866_F TGGTTATCGCT 617 RPOB_EC_1909_1929_TMOD_R TGCTGGATTCGCC 1250 CAGGCGAACTC TTTGCTACG CAAC 2030 RPLB_EC_650_679_TMOD_F TGACCTACAGT 449 RPLB_EC_739_763_R TGCCAAGTGCTGG 1208 AAGAGGTTCTG TTTACCCCATGG AATGAACC 2031 RPLB_EC_690_710_F TCCACACGGTG 309 RPLB_EC_737_760_R TGGGTGCTGGTTT 1295 GTGGTGAAGG ACCCCATGGAG 2032 INFB_EC_1366_1393_F TCTCGTGGTGC 397 INFB_EC_1439_1469_R TGTGCTGCTTTCG 1335 ACAAGTAACGG CATGGTTAATTGC ATATTA TTCAA 2033 VALS_EC_1105_1124_TMOD_F TCGTGGCGGCG 385 VALS_EC_1195_1219_R TGGGTACGAACTG 1292 TGGTTATCGA GATGTCGCCGTT 2034 SSPE_BA_113_137_F TGCAAGCAAAC 482 SSPE_BA_197_222_TMOD_R TTGCACGTCTGTT 1402 GCACAATCAGA TCAGTTGCAAATT AGC C 2035 RPOC_EC_2218_2241_TMOD_F TCTGGCAGGTA 405 RPOC_EC_2313_2338_R TGGCACCGTGGGT 1273 TGCGTTGTCTG TGAGATGAAGTAC ATG 2056 MECI-NC003923- TTTACACATAT 698 MECI-NC003923-41798- TTGTGATATGGAG 1420 41798-41609_33_60_F CGTGAGCAATG 41609_86_113_R GTGTAGAAGGTGT AACTGA TA 2057 AGR-III_NC003923- TCACCAGTTTG 263 AGR-III_NC003923- ACCTGCATCCCTA 730 2108074- CCACGTATCTT 2108074- AACGTACTTGC 2109508_1_23_F CAA 2109507_56_79_R 2058 AGR-III_NC003923- TGAGCTTTTAG 457 AGR-III_NC003923- TACTTCAGCTTCG 906 2108074- TTGACTTTTTC 2108074- TCCAATAAAAAAT 2109507_569_596_F AACAGC 2109507_622_653_R CACAAT 2059 AGR-III_NC003923- TTTCACACAGC 701 AGR-III_NC003923- TGTAGGCAAGTGC 1319 2108074- GTGTTTATAGT 2108074- ATAAGAAATTGAT 2109507_1024_1052_F TCTACCA 2109507_1070_1098_R ACA 2060 AGR- TGGTGACTTCA 610 AGR- TCCCCATTAATAA 1021 I_AJ617706_622_651_F TAATGGATGAA I_AJ617706_694_726_R TTCCACCTACTAT GTTGAAGT CACACT 2061 AGR- TGGGATTTTAA 579 AGR- TGGTACTTCAACT 1302 I_AJ617706_580_611_F AAAACATTGGT I_AJ617706_626_655_R TCATCCATTATGA AACATCGCAG AGTC 2062 AGR-II_NC002745- TCTTGCAGCAG 415 AGR-II_NC002745- TTGTTTATTGTTT 1424 2079448- TTTATTTGATG 2079448- CCATATGCTACAC 2080879_620_651_F AACCTAAAGT 2080879_700_731_R ACTTTC 2063 AGR-II_NC002745- TGTACCCGCTG 624 AGR-II_NC002745- TCGCCATAGCTAA 1077 2079448- AATTAACGAAT 2079448- GTTGTTTATTGTT 2080879_649_679_F TTATACGAC 2080879_715_745_R TCCAT 2064 AGR- TGGTATTCTAT 606 AGR- TGCGCTATCAACG 1233 IV_AJ617711_931_961_F TTTGCTGATAA IV_AJ617711_1004_1035_R ATTTTGACAATAT TGACCTCGC ATGTGA 2065 AGR- TGGCACTCTTG 562 AGR- TCCCATACCTATG 1017 IV_AJ617711_250_283_F CCTTTAATATT IV_AJ617711_309_335_R GCGATAACTGTCA AGTAAACTATC T A 2066 BLAZ_NC002952 TCCACTTATCG 312 BLAZ_NC002952 TGGCCACTTTTAT 1277 (1913827 . . . CAAATGGAAAA (1913827 . . . CAGCAACCTTACA 1914672)_68_68_F TTAAGCAA 1914672)_68_68_R GTC 2067 BLAZ_NC002952 TGCACTTATCG 494 BLAZ_NC002952 TAGTCTTTTGGAA 926 (1913827 . . . CAAATGGAAAA (1913827 . . . CACCGTCTTTAAT 1914672)_68_68_2_F 1914672)_68_68_2_R TAAAGT 2068 BLAZ_NC002952 TGATACTTCAA 467 BLAZ_NC002952 TGGAACACCGTCT 1263 (1913827 . . . CGCCTGCTGCT (1913827 . . . TTAATTAAAGTAT 1914672)_68_68_3_F TTC 1914672_68_68_3_F CTCC 2069 BLAZ_NC002952 TATACTTCAAC 232 BLAZ_NC002952 TCTTTTCTTTGCT 1145 (1913827 . . . GCCTGCTGCTT (1913827 . . . TAATTTTCCATTT 1914672)_68_68_4_F TC 1914672)_68_68_4_R GCGAT 2070 BLAZ_NC002952 TGCAATTGCTT 487 BLAZ_NC002952 TTACTTCCTTACC 1366 (1913827 . . . TAGTTTTAAGT (1913827 . . . ACTTTTAGTATCT 1914672)_1_33_F GCATGTAATTC 1914672)_34_67_R AAAGCATA 2071 BLAZ_NC002952 TCCTTGCTTTA 351 BLAZ_NC002952 TGGGGACTTCCTT 1289 (1913827 . . . GTTTTAAGTGC (1913827 . . . ACCACTTTTAGTA 1914672)_3_34_F ATGTAATTCAA 1914672)_40_68_R TCTAA 2072 BSA-A_NC003923- TAGCGAATGTG 214 BSA-A_NC003923- TGCAAGGGAAACC 1197 1304065- GCTTTACTTCA 1304065- TAGAATTACAAAC 1303589_99_125_F CAATT 1303589_165_193_R 2073 BSA-A_NC003923- ATCAATTTGGT 32 BSA-A_NC003923- TGCATAGGAAGG 1203 1304065- GGCCAAGAAC 1304065- TAACACCATAGTT 1303589_194_218_F CTGG 1303589_253_278_R 2074 BSA-A_NC003923- TTGACTGCGGC 679 BSA-A_NC003923- TAACAACGTTACC 856 1304065- ACAACACGGAT 1304065- TTCGCGATCCACT 1303589_328_349_F 1303589_388_415_R 2075 BSA-A_NC003923- TGCTATGGTGT 519 BSA-A_NC003923- TGTTGTGCCGCAG 1353 1304065- TACCTTCCCTA 1304065- TCAAATATCTAAAT 1303589_253_278_F TGCA 1303589_317_344_R 2076 BSA-B_NC003923- TAGCAACAAAT 209 BSA-B_NC003923- TGTGAAGAACTTT 1331 1917149- ATATCTGAAGC 1917149- CAAATCTGTGAAT 1914156_953_982_F AGCGTACT 1914156_1011_1039_R CCA 2077 BSA-B_NC003923- TGAAAAGTATG 426 BSA-B_NC003923- TCTTCTTGAAAAA 1138 1917149- GATTTGAACAA 1917149- TTGTTGTCCCGAA 1914156_1050_1081_F CTCGTGAATA 1914156_1109_1136_R AC 2078 BSA-B_NC003923- TCATTATCATG 300 BSA-B_NC003923- TGGACTAATAACA 1267 1917149- CGCCAATGAGT 1917149- ATGAGCTCATTGT 1914156_1260_1286_F GCAGA 1914156_1323_1353_R ACTGA 2079 BSA-B_NC003923- TTTCATCTTAT 703 BSA-B_NC003923- TGAATATGTAATG 1148 1917149- CGAGGACCCGA 1917149- CAAACCAGTCTTT 1914156_2126_2153_F ATCGA 1914156_2186_2216_R GTCAT 2080 ERMA_NC002952- TCGCTATCTTA 372 ERMA_NC002952- TGAGTCTACACTT 1174 55890- TCGTTGAGAAG 55890- AGGCTTAGGATGA 56621_366_392_F GGATT 56621_487_513_R A 2081 ERMA_NC002952- TAGCTATCTTA 217 ERMA_NC002952- TGAGCATTTTTAT 1167 55890- TCGTTGAGAAG 55890- ATCCATCTCCACC 56621_366_395_F GGATTTGC 56621_438_465_R AT 2082 ERMA_NC002952- TGATCGTTGAG 470 ERMA_NC002952- TCTTGGCTTAGGA 1143 55890- AAGGGATTTGC 55890- TGAAAATATAGTG 56621_374_402_F GAAAAGA 56621_473_504_R GTGGTA 2083 ERMA_NC002952- TGCAAAATCTG 480 ERMA_NC002952- TCAATACAGAGTC 964 55890- CAACGAGCTTT 55890- TACACTTGGCTTA 56621_404_427_F GG 56621_491_520_R GGAT 2084 ERMA_NC002952- TCATCCTAAGC 297 ERMA_NC002952- TGGACGATATTCA 1266 55890- CAAGTGTAGAC 55890- CGGTTTACCCACT 56621_489_516_F TCTGTA 56621_586_615_R TATA 2085 ERMA_NC002952- TATAAGTGGGT 231 ERMA_NC002952- TTGACATTTGCA 1397 55890- AAACCGTGAAT 55890- TGCTTCAAAGCCT 56621_586_614_F ATCGTGT 56621_640_665_R G 2086 ERMC_NC005908- TCTGAACATGA 399 ERMC_NC005908- TCCGTAGTTTTG 1041 2004- TAATATCTTTG 2004- CATAATTATGGT 2738_85_116_F AAATCGGCTC 2738_173_206_R CTATTTCAA 2087 ERMC_NC005908- TCATGATAATA 298 ERMC_NC005908- TTTATGGTCTAT 1429 2004- TCTTTGAAATC 2004- TTCAATGGCAGTT 2738_90_120_F GGCTCAGGA 2738_460_189_R ACGAA 2088 ERMC_NC005908- TCAGGAAAAGG 283 ERMC_NC005908- TATGGTCTATTT 936 2004- GCATTTTACCC 2004- CAATGGCAGTTAC 2738_115_139_F TTG 2738_161_187_R GA 2089 ERMC_NC005908- TAATCGTGGAA 168 ERMC_NC005908- TCAACTTCTGCC 956 2004- TACGGGTTTGC 2004- ATTAAAAGTAATG 2738_374_397_F TA 2738_325_452_R CCA 2090 ERMC_NC005908- TCTTTGAAATC 421 ERMC_NC005908- TGATGGTCTATT 1185 2004- GGCTCAGGAAA 2004- TCAATGGCAGTTA 2738_101_125_F AGG 2738_159_188_R CGAAA 2091 ERMB_Y13600-625- TGTTGGGAGTA 644 ERMB_Y13600-625- TCAACAATCAGA 953 1362_291_321_F TTCCTTACCAT 1362_352_380_R TAGATGTCAGACG TTAAGCACA CATG 2092 ERMB_Y13600-625- TGGAAAGCCAT 536 ERMB_Y13600-625- TGCAAGAGCAAC 1196 1362_344_367_F GCGTCTGACAT 1362_415_437_R CCTAGTGTTCG 2093 ERMB_Y13600-625- TGGATATTCAC 556 ERMB_Y13600-625- TAGGATGAAAGC 919 1363_404_429_F CGAACACTAGG 1362_471_493_R ATTCCGCTGGC 2094 ERMB_Y13600-625- TAAGCTGCCAG 161 ERMB_Y13600-625- TCATTCTGTGGTA 989 1362_465_487_F CGGAATGCTTT 1362_521_545_R TGGCGGGTAAGTT C 2095 PVLUK_NC003923- TGAGCTGCATC 456 PVLUK_NC003923- TGGAAAACTCAT 1261 1529595- ACTGTATTGGA 1529595- GAAATTAAAGTGA 1531285_688_713_F TAG 1531285_775_804_R AAGGA 2096 PVLUK_NC003923- TGGAACAAAAT 539 PVLUK_NC003923- TCATTAGGTAAAA 993 1529595- AGTCTCTCGGA 1529595- TGTCTGGACATG 1531285_1039_1068_F TTTTGACT 1531285_1095_1125_R ATCCAA 2097 PVLUK_NC003923- TGAGTAACATC 461 PVLUK_NC003923- TCTCATGAAAAAG 1124 1529595- CATATTTCTGC 1529595- GCTCAGGAGATAC 1531285_908_936_F CATACGT 1531285_950_978_R AAG 2098 PVLUK_NC003923- TCGGAATCTGA 373 PVLUK_NC003923- TCACACCTGTAAG 968 1529595- TGTTCAGTTGT 1529595- TGAGAAAAAGGTT 1531285_610_633_F TT 1531285_654_682_R TGAT 2099 SA442_NC003923- TGTCGGTACAC 635 SA442_NC003923- TTTCCGATCAAC 1433 2538576- GATATTCTTCA 2538576- GTAATGAGATTTC 25388311_35_F CGA 2538831_98_124_R A 2100 SA442_NC003923- TGAAATCTCAT 427 SA442_NC003923- TCGTATGACCAGC 1098 2538576- TACGTTGCATC 2538576- TTCGGTACTACTA 2538831_98_124_F G 2538831_163_188_R 2101 SA442_NC003923- TCTCATTACGT 395 SA442_NC003923- TTTATGACCAGCT 1428 2538576- TGCATCGGAAA 2538576- TCGGTACTACTAA 2538831_103_126_F CA 2538831_161_187_R A 2102 SA442_NC003923- TAGTACCGAAG 226 SA442_NC003923- TGATAATGAAGGG 1179 2538576- CTGGTCATACG 2538576- AAACCTTTTTCAC 2538831_166_188_F A G 2538831_231_257_R 2103 SEA_NC003923- TGCAGGGAACA 495 SEA_NC003923- TCGATCGTGACTC 1070 2052219- GCTTTAGGCA 2052219- TCTTTATTTTCAG 2051456_115_135_F 2051456_173_200_R TT 2104 SEA_NC003923- TAACTCTGATG 156 SEA_NC003923- TGTAATTAACCGA 1315 2052219- TTTTTGATGGG 2052219- AGGTTCTGTAGA 2051456_572_598_F AAGGT 2051456_621_651_R GTATG 2105 SEA_NC003923- TGTATGGTGGT 629 SEA_NC003923- TAACCGTTTCCA 861 2052219- GTAACGTTACA 2052219- AGGTACTGTATTT 2051456_382_414_F TGATAATAAT 2051456_464_492_R TGT C 2106 SEA_NC003923- TTGTATGTATG 695 SEA_NC003923- TAACCGTTTCCAA 862 2052219- GTGGTGTAACG 2052219- AGGTACTGTATTT 2051456_377_406_F TTACATGA 2051456_459_492_R TGTTTACC 2107 SEB_NC002758- TTTCACATGTA 702 SEB_NC002758- TCATCTGGTTTAG 988 2135540- ATTTTGATATT 2135540- GATCTGGTTGACT 2135140_208_137_F CGCACTGA 2135140_273_298_R 2108 SEB_NC002758- TATTTCACATG 244 SEB_NC002758- TGCAACTCATCTG 1194 2135540- TAATTTTGATA 2135540- GTTAGGATCT 2135140_106_235_F TTCGCACT 2135140_281_304_R 2109 SEB_NC002758- TAACAACTCGC 151 SEB_NC002758- TGTGCAGGCATCA 1334 2135540- CTTATGAAACG 2135540- TGTCATACCAA 2135140_402_402_F GGATATA 2135140_402_402_R 2110 SEB_NC002758- TTGTATGTATG 696 SEB_NC002758- TTACCATCTTCAA 1361 2135540- GTGGTGTAACT 2135540- ATACCCGAACAG 2135140_402_402_2_F GAGCA 2135140_402_402_2_R 2111 SEC_NC003923- TTAACATGAAG 648 SEC_NC003923- TGAGTTTGCACTT 1177 851678- GAAACCACTTT 851678- CAAAAGAAATTGT 852768_546_575_F GATAATGG 852768_620_647_R GT 2112 SEC_NC003923- TGGAATAACAA 546 SEC_NC003923- TCAGTTTGCACTT 985 851678- AACATGAAGGA 851678- CAAAAGAAATTGT 852768_537_566_F AACCACTT 852768_619_647_R GTT 2113 SEC_NC003923- TGAGTTTAACA 466 SEC_NC003923- TCGCCTGGTGCAG 1078 851678- GTTCACCATAT 851678- GCATCATAT 852768_720_749_F GAAACAGG 852768_794_815_R 2114 SEC_NC003923- TGGTATGATAT 604 SEC_NC003923- TCTTCACACTTTT 1133 851678- GATGCCTGCAC 851678- AGAATCAACCGTT 852768_787_810_F CA 852768_853_886_R TTATTGTC 2115 SED_M28521_657_ TGGTGGTGAAA 615 SED_M28521_ TGTACACCATTTA 1318 682_F TAGATAGGACT 741_770_R TCCACAAATTGAT GCTT TGGT 2116 SED_M28521_ TGGAGGTGTCA 554 SED_M28521_ TGGGCACCATTTA 1288 690_711_F ACTCCACACGA 739_770_R TCCACAAATTGAT A TGGTAT 2117 SED_M28521_ TTGCACAAGCA 683 SED_M28521_ TCGCGCTGTATTT 1079 833_854_F AGGCGCTATTT 888_911_R TTCCTCCGAGA 2118 SED_M28521_ TGGATGTTAAG 559 SED_M28521_ TGTCAATATGAAG 1320 962_987_F GGTGATTTTCC 1022_1048_R GTGCTCTGTGGAT CGAA A 2119 SEA-SEE_NC002952- TTTACACTACT 699 SEA-SEE_NC002952- TCATTTATTTCTT 994 2131289- TTTATTCATTG 2131289- CGCTTTTCTGCT 2130703_16_45_F CCCTAACG 2130703_71_98_R AC 2120 SEA-SEE_NC002952- TGATCATCCGT 469 SEA-SEE_NC002952- TAAGCACCATATA 870 2131289- GGTATAACGAT 2131289- AGTCTACTTTTTC 2130703_249_278_F TTATTAGT 2130703_314_344_R CCCTT 2121 SEE_NC002952- TGACATGATAA 445 SEE_NC002952- TCTATAGGTACT 1120 2131289- TAACCGATTGA 2131289- GTAGTTTGTTTTC 2130703_409_437_F CCGAAGA 2130703_485_494_R CGTCT 2122 SEE_NC002952- TGTTCAAGAGC 640 SEE_NC002952- TTTGCACCTTAC 1436 2131289- TAGATCTTCAG 2131289- CGCCAAAGCT 2130703_525_550_F GCAA 2130703588_588_R 2123 SEE_NC002952- TGTTCAAGAGC 639 SEE_NC002952- TACCTTACCGCC 892 2131289- TAGATCTTCAG 2131289- AAAGCTGTCT 2130703_525_549_F GCA 2130703_588_586_2_R 2124 SEE_NC002952- TCTGGAGGCAC 403 SEE_NC002952- TCCGTCTATCCA 1043 2131289- ACCAAATAAAA 2131289- CAAGTTAATTGGT 2130703_381_384_F CA 2130703_444_471_R ACT 2125 SEG_NC002758- TGCTCAACCCG 520 SEG_NC002758- TAACTCCTCTTCC 863 1955100- ATCCTAAATTA 1955100- TTCAACAGGTGGA 1954171_225_251_F GACGA 1954171_321_348_R 2126 SEG_NC002758- TGGACAATAGA 548 SEG_NC002758- TGCTTTGTAATC 1260 1955100- CAATCACCTTG 1955100- AGTTCCTGAATAG 1954171_623_851_F GATTTACA 1954171_871_702_R TAACCA 2127 SEG_NC002758- TGGAGGTTGTT 555 SEG_NC002758- TGTCTATTGTCGA 1329 1955100- GTATGTATGG 1955100- ATTGTTACCTGTA 1954171_540_584_F TGTT 1954171_607_635_R CAGT 2128 SEG_NC002758- TACAAAGCAAG 173 SEG_NC002758- TGATTCAAATGCA 1187 1955100- ACACTGGCTC 1955100- GAACCATCAAACT 1954171_694_718_F ACTA 1954171_735_782_R CG 2129 SEH_NC002953- TTGCAACTGCT 682 SEH_NC002953- TAGTGTTGTACCT 927 60024- GATTTAGCTCA 60024- CCATATAGACATT 60977_449_472_F GA 60977_547_578_R CAGA 2130 SEH_NC002953- TAGAAATCAAG 201 SEH_NC002953- TTCTGAGCTAAAT 1390 60024- GTGATAGTGGC 60024- ACAGCAGTTGC 60977_408_434_F AAATGA 60977_450_473_R 2131 SEH_NC002953- TCTGAARTGTC 400 SEH_NC002953- TACCATCTACCC 888 60024- TATATGGAGGT 60024- AACATTAGCACCA 60977_547_576_F ACAACACTA 60977_608_634_R A 2132 SEH_NC002953- TTCTGAATGTC 677 SEH_NC002953- TAGCACCAATCAC 909 60024- TATATGGAGGT 60024- CCTTTCCTGT 60977_546_575_F ACAACACT 60977_594_616_R 2133 SEI_NC002758- TCAACTCGAAT 253 SEI_NC002758- TCACAAGGACCAT 966 1957830- TTTCAACAGGT 1957830- TATAATCAATGCC 1956949_324_349_F ACCA 1956949_419_448_R AA 2134 SEI_NC002758- TTCAACAGGTA 666 SEI_NC002758- TGTACAAGGACCA 1316 1957830- CCAATGATTTG 1957830- TTATAATCAATGC 1956949_336_363_F ATCTCA 1958949_420_447_R CA 2135 SEI_NC002758- TGATCTCAGAA 471 SEI_NC002758- TCTGGCCCCTCCA 1129 1957830- TCTAATAATTG 1957830- TACATGTATTTAG 1956949_356_384_F GGACGAA 1958949_449_474_R 2136 SEI_NC002758- TCTCAAGGTGA 394 SEI_NC002758- TGGGTAGGTTTTT 1293 1957830- TATTGGTGTAG 1957830- ATCTGTGACGCCT 1956949_223_253_F GTAACTTAA 1958949_290_316_R T 2137 SEJ_AF053140- TGTGGAGTAAC 637 SEJ_AF053140- TCTAGCGGAACAA 1118 1307_1332_F ACTGCATGAAA 1381_1404_R CAGTTCTGATG ACAA 2138 SEJ_AF053140- TAGCATCAGAA 211 SEJ_AF053140- TCCTGAAGATCTA 1049 1378_1403_F CTGTTGTTCCG 1429_1458_R GTTCTTGAATGGT CTAG TACT 2139 SEJ_AF053140- TAACCATTCAA 153 SEJ_AF053140- TAGTCCTTTCTGA 925 1431_1459_F GAACTAGATCT 1500_1531_R ATTTACCATCAA TCAGGCA AGGTAC 2140 SEJ_AF053140- TCATTCAAGAA 301 SEJ_AF053140- TCAGGTATGAAAC 984 1434_1461_F CTAGATCTTCA 1521_1549_R ACGATTAGTCCTT GGCAAG TCT 2141 TSST_NC002758- TGGTTTAGATA 619 TSST_NC002758- TGTAAAAGCAGGG 1312 2137564- ATTCTTTAGGA 2137564- CTATAATAAGGAC 2138293_206_236_F TCTATGCGT 2138293_278_305_R TC 2142 TSST_NC002758- TGCGTATAAAA 514 TSST_NC002758- TGCCCTTTTGTAA 1221 2137564- AACACAGATGG 2137564- AAGCAGGGCTAT 2138293_232_258_F CAGCA 2138293_289_313_R 2143 TSST_NC002758- TCCAAATAAGT 304 TSST_NC002758- TACTTTAAGGGGC 907 2137564- GGCGTTACAAA 2137564- TATCTTTACCATG 2138293_382_410_F TACTGAAA 2138293_448_478_R AACCT 2144 TSST_NC002758- TCTTTTACAAA 423 TSST_NC002758- TAAGTTCCTTCGC 874 2137564- AGGGGAAAAG 2137564- TAGTATGTTGGCT 2138293_297_325_F TTGACTT 2138293_347_373_R T 2145 ARCC_NC003923- TCGCCGGCAAT 368 ARCC_NC003923- TGAGTTAAAATGC 1175 2725050- GCCATTGGATA 2725050- GATTGATTTCAGT 2724595_37_58_F 2724595_97_128_R 2146 ARCC_NC003923- TGAATAGTGAT 437 ARCC_NC003923- TCTTCTTCTTCG 1137 2725050- AGAACTGTAGG 2725050- TATAAAAAGGACC 2724595_131_161_F CACAATCGT 2724595_214_245_R AATTGG 2147 ARCC_NC003923- TTGGTCCTTTT 691 ARCC_NC003923- TGGTGTTCTAGTA 1306 2725050- TATACGAAAGA 2725050- TAGATTGAGGTAG 2724595_218_249_F AGAAGTTGAA 2724595_322_353_R TGGTGA 2148 AROE_NC003923- TTGCGAATAGA 686 AROE_NC003923- TCGAATTCAGCTA 1064 1674726- ACGATGGCTCG 1674726- AATACTTTTCAGC 1674277_371_393_F T 1674277_435_464_R ATCT 2149 AROE_NC003923- TGGGGCTTTAA 590 AROE_NC003923- TACCTGCATTAAT 891 1674726- ATATTCCAATT 1674726- CGCTTGTTCATCA 1674277_30_62_F GAAGATTTTCA 1674277_155_181_R A 2150 AROE_NC003923- TGATGGCAAGT 474 AROE_NC003923- TAAGCAATACCTT 869 1674726- GGATAGGGTAT 1674726- TACTTGCACCACC 1674277_204_232_F AATACAG 1674277_308_335_R TTG 2151 GLPF_NC003923- TGCACCGGCTA 491 GLPF_NC003923- TGCAACAATTAAT 1193 1296927- TTAAGAATTAC 1296927- GCTCCGACAATTA 297391_270_301_F TTTGCCAACT 1297391_382_414_R AAGGATT 2152 GLPF_NC003923- TGGATGGGGAT 558 GLPF_NC003923- TAAAGACACCGCT 850 1296927- TAGCGGTTACA 1296927- GGGTTTAAATGTG 1297391_27_51_F ATG 1297391_81_108_R CA 2153 GLPF_NC003923- TAGCTGGCGCG 218 GLPF_NC003923- TCACCGATAAATA 972 1296927- AAATTAGGTGT 1296927- AAATACCTAAAGT 1297391_239_260_F 1297391_323_359_R TAATGCCATTG 2154 GMK_NC003923- TACTTTTTTAA 200 GMK_NC003923- TGATATTGAACTG 1180 1190906- AACTAGGGATG 1190906- GTGTACCATAATA 119334_91_122_F CGTTTGAAGC 1191334_166_197_R GTTGCC 2155 GMK_NC003923- TGAAGTAGAAG 435 GMK_NC003923- TCGCTCTCTCAAG 1082 1190906- GTGCAAAGCAA 1190906- TGATCTAAACTTG 1191334_240_267_F GTTAGA 1191334_305_333_R GAG 2156 GMK_NC003923- TCACCTCCAAG 268 GMK_NC003923- TGGGACGTAATCG 1284 1190906- TTTAGATCACT 1190906- TATAAATTCATCA 1191334_301_329_F TGAGAGA 1191334_403_432_R TTTC 2157 PTA_NC003923- TCTTGTTTATG 418 PTA_NC003923- TGGTACACCTGGT 1301 628885- CTGGTAAAGCA 628885- TTCGTTTTGATGA 629355_237_263_F GATGG 629355_314_345_R TTTGTA 2158 PTA_NC003923- TGAATTAGTTC 439 PTA_NC003923- TGCATTGTACCGA 1207 628885- AATCATTTGTT 628885- AGTAGTTCACATT 629355_141_171_F GAACGACGT 629355_211_239_R GTT 2159 PTA_NC003923- TCCAAACCAGG 303 PTA_NC003923- TGTTCTGGATTGA 1349 628885- TGTATCAAGAA 628885- TTGCACAATCACC 629355_328_356_F CATCAGG 629355_393_422_R AAAG 2160 TPI_NC003923- TGCAAGTTAAG 486 TPI_NC003923- TGAGATGTTGATG 1165 830671- AAAGCTGTTGC 830671- ATTACCAGTTCC 831072_131_160_F AGGTTTAT 831072_209_239_R GATTG 2161 TPI_NC003923- TCCCACGAAAC 318 TPI_NC003923- TGGTACAACATCG 1300 830671- AGATGAAGAAA 830671- TTAGCTTTACCAC 831072_1_34_F TTAACAAAAAA 831072_97_129_R TTTCACG G 2162 TPI_NC003923- TCAAACTGGGC 246 TPI_NC003923- TGGCAGCAATAGT 1275 830671- AATCGGAACTG 830671- TTGACGTACAAAT 831072_199_227_F GTAAATC 831072_253_286_R GCACACAT 2163 YQI_NC003923- TGAATTGCTGC 440 YQI_NC003923- TCGCCAGCTAGCA 1076 378916- TATGAAAGGTG 378916- CGATGTCATTTTC 379431_142_167_F GCTT 379431_259_284_R 2164 YQI_NC003923- TACAACATATT 175 YQI_NC003923- TTCGTGCTGGATT 1388 378916- ATTAAAGAGAC 378916- TTGTCCTTGTCCT 379431_44_77_F GGGTTTGAATC 379431_120_145_R C 2165 YQI_NC003923- TCCAGCACGAA 314 YQI_NC003923- TCCAACCCAGAAC 997 378916- TTGCTGCTATG 378916- CACATACTTTATT 379431_135_160_F AAAG 379431_193_221_R CAC 2166 YQI_NC003923- TAGCTGGCGGT 219 YQI_NC003923- TCCATCTGTTAAA 1013 378916- ATGGAGAATAT 378916- CCATCATATACCA 379431_275_300_F GTCT 379431_364_396_R TGCTATC 2167 BLAZ_ TCCACTTATCG 312 BLAZ_ TGGCCACTTTTAT 1277 (1913827 . . . CAAATGGAAAA (1913827 . . . CAGCAACCTTACA 1914672)_546_ TTAAGCAA 1914672)_655_ GTC 575_F 683_R 2168 BLAZ_ TGCACTTATCG 494 BLAZ_ TAGTCTTTTGGAA 926 (1913827 . . . CAAATGGAAAA (1913827 . . . CACCGTCTTTAAT 1914672)_546_ TTAAGCAA 1914672)_628_ TAAAGT 575_2_F 659_R 2169 BLAZ_ TGATACTTCAA 467 BLAZ_ TGGAACACCGTCT 1263 (1913827 . . . CGCCTGCTGCT (1913827 . . . TTAATTAAAGTAT 1914672)_507_ TTC 1914672)_622_ CTCC 531_F 651_R 2170 BLAZ_ TATACTTCAAC 232 BLAZ_ TCTTTTCTTGCT 1145 (1913827 . . . GCCTGCTGCTT 1913827 . . . TAATTTTCCATTT 1914672)_508_ TC 1914672)_553_ GCGAT 531_F 583_R 2171 BLAZ_ TGCAATTGCTT 487 BLAZ_ TTACTTCCTTACC 1366 (1913827 . . . TAGTTTTAAGT (1913827 . . . CTTTTAGTATCT 1914672)_24_ GCATGTAATTC 1914672)_121_ AAAGCATA 56_F 154_R 2172 BLAZ_ TCCTTGCTTTA 351 BLAZ_ TGGGGACTTCCTT 1289 (1913827 . . . 1914672)_ GTTTTAAGTGC (1913827 . . . 1914672)_ ACCACTTTTAGTA 26_58_F ATGTAATTCAA 127_157_R TCTAA 2173 BLAZ_NC002952- TCCACTTATCG 312 BLAZ_NC002952- TGGCCACTTTTAT 1277 1913827- CAAATGGAAAA 1913827- CAGCAACCTTACA 1914672_546_575_F TTAAGCAA 1914672_655_683_R GTC 2174 BLAZ_NC002952- TGCACTTATCG 494 BLAZ_NC002952- TAGTCTTTTGGAA 926 1913827- CAAATGGAAAA 1913827- CACCGTCTTTAAT 1914672_546_575_2_F TTAAGCAA 1914672_628_659_R TAAAGT 2175 BLAZ_NC002952- TGATACTTCAA 467 BLAZ_NC002952- TGGAACACCGTCT 1263 1913827- CGCCTGCTGCT 1913827- TTAATTAAAGTAT 1914672_507_531_F TTC 1914672_622_651_R CTCC 2176 BLAZ_NC002952- TATACTTCAAC 232 BLAZ_NC002952- TCTTTTCTTTGCT 1145 1913827- GCCTGCTGCTT 1913827- TAATTTTCCATTT 1914672_508_531_F TC 1914672_553_583_R GCGAT 2177 BLAZ_NC002952- TGCAATTGCTT 487 BLAZ_NC002952- TTACTTCCTTACC 136 1913827- TAGTTTTAAGT 1913827- ACTTTTAGTATCT 1914672_24_56_F GCATGTAATTC 1914672_121_154_R AAAGCATA 2178 BLAZ_NC002952- TCCTTGCTTTA 351 BLAZ_NC002952- TGGGGACTTCCTT 1289 1913827- GTTTTAAGTGC 1913827- ACCACTTTTAGTA 1914672_26_58_F ATGTAATTCAA 1914672_127_157_R TCTAA 2247 TUFB_NC002758- TGTTGAACGTG 643 TUFB_NC002758- TGTCACCAGCTTC 1321 615038- GTCAAATCAAA 615038- AGCGTAGTCTAA 616222_693_721_F GTTGGTG 616222_793_820_R TAA 2248 TUFB_NC002758- TCGTGTTGAAC 386 TUFB_NC002758- TGTCACCAGCTTC 1321 615038- GTGGTCAAATC 615038- AGCGTAGTCTAAT 616222_690_716_F AAAGT 616222_793_820_R AA 2249 TUFB_NC002758- TGAACGTGGTC 430 TUFB_NC002758- TGTCACCAGCTTC 1321 615038- AAATCAAAGTT 615038- AGCGTAGTCTAAT 616222_696_725_F GGTGAAGA 616222_793_820_R AA 2250 TUFB_NC002758- TCCCAGGTGAC 320 TUFB_NC002758- TGGTTTGTCAGAA 1311 615038- GATGTACCTGT 615038- TCACGTTCTGGAG 616222_488_513_F AATC 616222_601_630_R TTGG 2251 TUFB_NC002758- TGAAGGTGGAC 433 TUFB_NC002758- TAGGCATAACCAT 922 615038- GTCACACTCCA 615038- TTCAGTACCTTCT 616222_945_972_F TTCTTC 616222_1030_1060_R GGTAA 2252 TUFB_NC002758- TCCAATGCCAC 307 TUFB_NC002758- TTCCATTTCAACT 1382 615038- AAACTCGTAA 615038- AATTCTAATAATT 616222_333_356_F CA 616222_424_459_R CTTCATCGTC 2253 NUC_NC002758- TCCTGAAGCAA 342 NUC_NC002758- TACGCTAAGCCAC 899 894288- GTGCATTTTAC 894288- GTCCATATTTATC 894974_402_424_F GA 894974_483_509_R A 2254 NUC_NC002758- TCCTTATAGGG 349 NUC_NC002758- TGTTTGTGATGCA 1354 894288- ATGGCTATCAG 894288- TTTGCTGAGCTA 894974_53_81_F TAATGTT 894974_165_189_R 2255 NUC_NC002758- TCAGCAAATGC 273 NUC_NC002758- TAGTTGAAGTTGC 928 894288- ATCACAAACAG 894288- ACTATATACTGTT 894974_169_194_F ATAA 894974_222_250_R GGA 2256 NUC_NC002758- TACAAAGGTCA 174 NUC_NC002758- TAAATGCACTTGC 853 894288- ACCAATGACAT 894288- TTCAGGGCCATAT 894974_316_345_F TCAGACTA 89474_396_421_R 2270 RPOB_EC_3798_3821_1_F TGGCCAGCGCT 566 RPOB_EC_3868_3895_R TCACGTCGTCCGA 979 TCGGTGAAATG CTTCACGGGTCAG GA CT 2271 RPOB_EC_3789_3812_F TCAGTTCGGCG 294 RPOB_EC_3860_3890_R TCGTCGGACTTAA 1107 GTCAGCGCTTC CGGTCAGCATTTC GG CTGCA 2272 RPOB_EC_3789_3812_F TCAGTTCGGCG 294 RPOB_EC_3860_3890_2_R TCGTCCGACTTAA 1102 GTCAGCGCTTC CGGTCAGCATTTC GG CTGCA 2273 RPOB_EC_3789_3812_F TCAGTTCGGCG 294 RPOB_EC_3862_3890_R TCGTCGGACTTAA 1106 GTCAGCGCTTC CGGTCAGCATTTC GG CTG 2274 RPOB_EC_3789_3812_F TCAGTTCGGCG 294 RPOB_EC_3862_3890_R TCGTCCGACTTAA 1101 GTCAGCGCTTC CGGTCAGCATTTC GG CTG 2275 RPOB_EC_3793_3812_F TTCGGCGGTCA 674 RPOB_EC_3865_3890_R TCGTCGGACTTAA 1105 GCGCTTCGG CGGTCAGCATTTC 2276 RPOB_EC_3793_3812_F TTCGGCGGTCA 674 RPOB_EC_3865_3890_R TCGTCCGACTTAA 1100 GCGCTTCGG CGGTCAGCATTTC 2309 MUPR_X75439_1658_1689_F TCCTTTGATAT 352 MUPR_X75439_1744_1773_R TCCCTTCCTTAT 1030 ATTATGCGATG ATGAGAAGGAAAC GAAGGTTGGT CACT 2310 MUPR_X75439_1330_1353_F TTCCTCCTTTT 669 MUPR_X75439_1413_1441_R TGAGCTGGTGCTA 1171 GAAAGCGACGG TATGAACAATACC TT AGT 2312 MUPR_X75439_1314_1338_F TTTCCTCCTTT 704 MUPR_X75439_1381_1409_R TATATGAACAATA 931 TGAAAGCGAC CCAGTTCCTTCTG GGTT AGT 2313 MUPR_X75439_2486_2516_F TAATTGGGCTC 172 MUPR_X75439_2548_2574_R TTAATCTGGCGT 1360 TTTCTCGCTTA GGAAGTGAAATCG AACACCTTA T 2314 MUPR_X75439_2547_2572_F TACGATTTCAC 188 MUPR_X75439_2605_2630_R TCGTCCTCTCGAA 1103 TTCCGCAGCCA TCTCCGATATACC GATT 2315 MUPR_X75439_2666_2696_F TGCGTACAATA 513 MUPR_X75439_2711_2740_R TCAGATATAAATG 981 CGCTTTATGAA GAACAAATGGAGC ATTTTAACA CACT 2316 MUPR_X75439_2813_2843_F TAATCAAGCAT 165 MUPR_X75439_2867_2890_R TCTGCATTTTTGC 1127 TGGAAGATGAA GAGCCTGTCTA ATGCATACC 2317 MUPR_X75439_884_914_F TGACATGGACT 447 MUPR_X75439_977_1007_R TGTACAATAAGGA 1317 CCCCCTATATA GTCACCTTATGTC ACTCTTGAG CCTTA 2318 CTXA_NC002505- TGGTCTTATGC 608 CTXA_NC002505- TCGTGCCTAACAA 1109 1568114- CAAGAGGACAG 1568114- ATCCCGTCTGAGT 1567341_114_142_F AGTGAGT 1567341_194_221_R TC 2319 CTXA_NC002505- TCTTATGCCAA 411 CTXA_NC002505- TCGTGCCTAACAA 1109 1568114- GAGGACAGAGT 1568114- ATCCCGTCTGAGT 1567341_117_145_F GAGTACT 1567341_194_221_R TC 2320 CTXA_NC002505- TGGTCTTATGC 608 CTXA_NC002505- TAACAAATCCCGT 855 1568114- CAAGAGGACAG 1568114- CTGAGTTCCTCTT 1567341_114_142_F AGTGAGT 1567341_186_214_R GCA 2321 CTXA_NC002505- TCTTATGCCAA 411 CTXA_NC002505- TAACAAATCCGT 855 1568114- GAGGACAGAGT 1568114- CTGAGTTCCTCTT 1567341_117_145_F GAGTACT 1567341_186_214_R GCA 2322 CTXA_NC002505- AGGACAGAGTG 27 CTXA_NC002505- TCCCGTCTGAGTT 1027 1568114- AGTACTTTGAC 1568114- CCTCTTGCATGAT 1567341_129_156_F CGAGGT 1567341_180_207_R CA 2323 CTXA_NC002505- TGCCAAGAGGA 500 CTXA_NC002505- TAACAAATCCCGT 855 1568114- CAGAGTGAGTA 1568114- CTGAGTTCCTCTT 1567341_122_149_F CTTTGA 1567341_186_214_R GCA 2324 INV_U22457-74- TGCTTATTTAC 530 INV_U22457-74- TGACCCAAAGCT 1154 3772_831_858_F CTGCACTCCCA 3772_942_966_R AAAGCTTTACTG CAACTG 2325 INV_U22457-74- TGAATGCTTAT 438 INV_U22457-74- TAACTGACCCAAA 864 3772_827_857_F TTACCTGCACT 3772_942970_R GCTGAAAGCTTTA CCCACAACT CTG 2326 INV_U22457-74- TGCTGGTAACA 526 INV_U22457-74- TGGGTTGCGTTG 1296 3772_1555_1581_F GAGCCTTATAG 3772_1619_1647_R AGATTATCTTTAC GCGCA CAA 2327 INV_U22457-74- TGGTAACAGAG 598 INV_U22457-74- TCATAAGGGTTG 987 3772_1558_1585_F CCTTATAGGCG 3772_1622_1652_R GTTGCAGATTATC CATATG TTTAC 2328 ASD_NC006570- TGAGGGTTTTA 459 ASD_NC006570- TGATTCGATCATA 1188 439714- TGCTTAAAGTT 439714- CGAGACATTAAA 438608_3_37_F GGTTTTATTGG 438608_54_84_R CTGAGT TT 2329 ASD_NC006570- TAAAGTTGGTT 149 ASD_NC006570- TCAAAATCTTTTG 948 439714- TTATTGGTTGG 439714- ATTCGATCATACG 438608_18_45_F CGCGGA 438608_66_95_R AGAC 2330 ASD_NC006570- TTAAAGTTGGT 647 ASD_NC006570- TCCCAATCTTTTG 1016 439714- TTTATTGGTTG 439714- ATTCGATCATACG 438608_17_45_F GCGCGGA 438608_67_95_R AGA 2331 ASD_NC006570- TTTTATGCTTA 709 ASD_NC006570- TCTGCCTGAGATG 1128 439714- AAGTTGGTTTT 439714- TCGAAAAAACGT 438608_9_40_F ATTGGTTGGC 438608_107_134_R TG 2332 GALE_AF513299_171_200_F TCAGCTAGACC 280 GALE_AF513299_241_271_R TCTCACCTACAGC 1122 TTTTAGGTAAA TTTAAAGCCAGCA GCTAAGCT AAATG 2333 GALE_AF513299_168_199_F TTATCAGCTAG 658 GALE_AF513299_245_271_R TCTCACCTACAG 1121 ACCTTTTAGGT TTTAAAGCCAGCA AAAGCTAAGC A 2334 GALE_AF513299_168_199_F TTATCAGCTAG 658 GALE_AF513299_233_264_R TACAGCTTTAAAG 883 ACCTTTTAGGT CCAGCAAAATGAA AAAGCTAAGC TTACAG 2335 GALE_AF513299_169_198_F TCCCAGCTAGA 319 GALE_AF513299_252_279_R TTCAACACTCTCA 1374 CCTTTTAGGTA CCTACAGCTTTAA AAGCTAAG AG 2236 PLA_AF053945_7371_7403_F TTGAGAAGACA 680 PLA_AF053945_7434_7468_R TACGTATGTAAAT 900 TCCGGCTCACG TCCGCAAAGACTT TTATTATGGTA TGGCATTAG 2337 PLA_AF053945_7377_7403_F TGACATCCGGC 443 PLA_AF053945_7428_7455_R TCCGCAAAGACTT 1035 TCACGTTATTA TGGCATTAGGTGT TGGTA GA 2338 PLA_AF053945_7377_7404_F TGACATCCGGC 444 PLA_AF053945_7430_7460_R TAAATTCCGCAAA 854 TCACGTTATTA GACTTTGGCATTA TGGTAC GGTGT 2339 CAF_AF053947_33412_33441_F TCCGTTATCGC 329 CAF_AF053947_33498_33523_R TAAGAGTGATGC 866 CATTGCATTAT GGCTGGTTCAACA TTGGAACT 2340 CAF_AF053947_33426_33458_F TGCATTATTTG 499 CAF_AF053947_33483_33507_R TGGTTCAACAAG 1308 GAACTATTGCA GTTGCCGTTGCA ACTGCTAATGC 2341 CAF_AF053947_33407_33429_F TCAGTTCCGTT 291 CAF_AF053947_33483_33504_R TTCAACAAGAGTT 1373 ATCGCCATTGC GCCGTTGCA A 2342 CAF_AF053947_33407_33431_F TCAGTTCCGTT 293 CAF_AF053947_33494_33517_R TGATGCGGGCTGG 1184 ATCGCCATTG TTCAACAAGAG CATT 2344 GAPA_NC_002505_1_28_F_1 TCAATGAACGA 260 GAPA_NC_002505_29_58_R_1 TCCTTTATGCAAC 1060 TCAACAAGTGA TTGGTATCAACAG TTGATG GAAT 2472 OMPA_NC000117_68_89_F TGCCTGTAGGG 507 OMPA_NC000117_145_167_R TCACACCAAGTAG 967 AATCCTGCTGA TGCAAGGATC A 2473 OMPA_NC000117_798_821_F TGATTACCATG 475 OMPA_NC000117_865_893_R TCAAAACTTGCTC 947 AGTGGCAAGCA TAGACCATTTAAC AG TCC 2474 OMPA_NC000117_645_671_F TGCTCAATCTA 521 OMPA_NC000117_757_777_R TGTCGCAGCATCT 1328 AACCTAAAGTC GTTCCTGC GAAGA 2475 OMPA_NC000117_947_973_F TAACTGCATGG 157 OMPA_NC000117_1011_1040_R TGACAGGACACAA 1153 AACCCTTCTTT TCTGCATGAAGTC ACTAG TGAG 2476 OMPA_NC000117_774_795_F TACTGGAACAA 196 OMPA_NC000117_871_894_R TTCAAAAGTTGCT 1371 AGTCTGCGACC CGAGACCATTG 2477 OMPA_NC000117_457_483_F TTCTATCTCGT 676 OMPA_NC000117_511_534_R TAAAGAGACGTTT 851 TGGTTTATTCG GGTAGTTCATTTG GAGTT C 2478 OMPA_NC000117_687_710_F TAGCCCAGCAC 212 OMPA_NC000117_787_816_R TTGCCATTCATGG 1406 AATTTGTGATT TATTTAAGTGTAG CA AGA 2479 OMPA_NC000117_540_566_F TGGCGTAGTAG 571 OMPA_NC000117_649_672_R TTCTTGAACGCGA 1395 AGCTATTTACA GGTTTCGATTG GACAC 2480 OMPA_NC000117_338_360_F TGCACGATGCG 492 OMPA_NC000117_417_444_R TCCTTTAAAATAA 1058 GAATGGTTCAC CCGCTAGTAGCTC A CT 2481 OMP2_NC000117_18_40_F TATGACCAAAC 234 OMP2_NC000117_71_91_R TCCCGCTGGCAAA 1025 TCATCAGACGA TAAACTCG G 2482 OMP2_NC000117_354_382_F TGCTACGGTAG 516 OMP2_NC000117_445_471_R TGGATCACTGCTT 1270 GATCTCCTTAT ACGAACTCAGCTT CCTATTG C 2483 OMP2_NC000117_1297_1319_F TGGAAAGGTGT 537 OMP2_NC000117_1396_1419_R TACGTTTGTATCT 903 TGCAGCTACTC TCTGCAGAACC A 2484 OMP2_NC000117_1465_1493_F TCTGGTCCAAC 407 OMP2_NC000117_1541_1569_R TCCTTTCAATGTT 1062 AAAAGGAACGA ACAGAAAACTCTA TTACAGG CAG 2485 OMP2_NC000117_44_66_F TGACGATCTTC 450 OMP2_NC000117_120_148_R TGTCAGCTAAGC 1323 GCGGTGACTAG TAATAACGTTTGT T AGAG 2486 OMP2_NC000117_166_190_F TGACAGCGAAG 441 OMP2_NC000117_240_261_R TTGACATCGTCCC 1396 AAGGTTAGACT TCTTCACAG TGTCC 2487 GYRA_NC000117_514_536_F TCAGGCATTGC 287 GYRA_NC000117_640_660_R TGCTGTAGGGAAA 1251 GGTTGGGATGG TCAGGGCC 2488 GYRA_NC000117_801_827_F TGTGAATAAAT 636 GYRA_NC000117_871_893_R TTGTCAGACTCAT 1419 CACGATTGATT CGCGAACATC GAGCA 2489 GYRA_NC002952_219_242_F TGTCATGGGTA 632 GYRA_NC002952_319_345_R TCCATCCATAGAA 1010 AATATCACCCT CCAAAGTTACCTT CA G 2490 GYRA_NC002952_964_983_F TACAAGCACTC 176 GYRA_NC002952_1024_1041_R TCGCAGCGTGCGT 1073 CCAGCTGCA GGCAC 2491 GYRA_NC002952_1505_1520_F TCGCCCGCGAG 366 GYRA_NC002952_1546_1562_R TTGGTGCGCTTGG 1416 GACGT CGTA 2492 GYRA_NC002952_59_81_F TCAGCTACATC 279 GYRA_NC002952_124_143_R TGGCGATGCACTG 1279 GACTATGCGAT GCTTGAG G 2493 GYRA_NC002952_216_239_F TGACGTCATCG 452 GYRA_NC002952_313_333_R TCCGAAGTTGCCC 1032 GTAAGTACCAC TGGCCGTC CC 2494 GYRA_NC002952_219_242_2_F TGTACTCGGTA 625 GYRA_NC002952_308_330_R TAAGTTACCTTGC 873 AGTATCACCCG CCGTCAACCA CA 2495 GYRA_NC002952_115_141_F TGAGATGGATT 453 GYRA_NC002952_220_242_R TGCGGGTGATACT 1236 TAAACCTGTTC TACCGAGTAC ACCGC 2496 GYRA_NC002952_517_5_39_F TCAGGCATTGC 287 GYRA_NC002952_643_663_R TGCTGTAGGGAAA 1251 GGTTGGGATGG TCAGGGCC C 2497 GYRA_NC002952_273_2_93_F TCGTATGGCTC 380 GYRA_NC002952_338_360_R TGCGGCAGCACTA 1234 AATGGTGGAG TCACCATCCA 2498 GYRA_NC000912_257_278_F TGAGTAAGTT 462 GYRA_NC000912_346_370_R TCGAGCCGAAGTT 1067 CCACCCGCACG CCCTGTCCGTC G 2504 ARCC_NC003923- TAGTpGATpAG 229 ARCC_NC003923-2725050- TCpTpTpTpCpGT 1116 2725050- AACpTpGTAGG 2724595_214_239P_R ATAAAAAGGACpC 2724595_135_161P_F CpACpAATpCp pAATpTpGG GT 2505 PTA_NC003923- TCTTGTpTpTp 417 PTA_NC003923-628885- TACpACpCpTGGT 904 629355_629355_237_263P_F ATGCpTpGGTA pTpTpCpGTpTpT AAGCAGATGG pTpGATGATpTpT pGTA 2517 CJMLST_ST1_1852_1883_F TTTGCGGATGA 708 CJMLST_ST1_1945_1977_R TGTTTTATGTG 1355 AGTAGGTGCCT TAGTTGAGCTTAC ATCTTTTTGC TTACTACATGAGC 2518 CJMLST_ST1_2963_2992_F TGAAATTGCTA 428 CJMLST_ST1_3073_3097_R TCCCCATCTCCGCA 1020 CAGGCCCTTTA AAGACAATAAA GGACAAGG 2519 CJMLST_ST1_2350_2378_F TGCTTTTGATG 535 CJMLST_ST1_2447_2481_R TCTACAACACT 1117 GTGATGCAGA TGATTGTAATTTG TCGTTTGG CCTTGTTCTTT 2520 CJMLST_ST1_654_684_F TATGTCCAAGA 240 CJMSLT_ST1_725_756_R TCGGAAACAAAGA 1084 AGCATAGCAAA ATTCATTTTCTGG AAAAGCAAT TCCAAA 2521 CJMSLT_ST1_360_395_F TCCTGTTATTC 347 CJMLST_ST1_454_457_R TGCTATATGCTAC 1245 CTGAAGTAGTT AACTGGTTCAAAA AATCAAGTTTG ACATTAAG TTA 2522 CJMSLT_ST1_1231_1258_F TGGCAGTTTTA 564 CJMSLT_ST1_1312_1340_R TTTAGCTACTATT 1427 CAAGGTGCTGT CTAGCTGCCATTT TTCATC CCA 2523 CJMSLT_ST1_3543_3574_F TGCTGTAGCTT 529 CJMLST_ST1_3656_3685_R TCAAAGAACCAGC 1427 ATCGCGAAATG ACCTAATTCATCA TCTTTGATTT TTTA 2524 CJMLST_ST1_1_17_F TAAAACTTTTG 145 CJMSLT_ST1_55_84_R TGTTCCAATAGCA 1348 CCGTAATGATG GTTCCGCCCAAAT GGTGAAGATAT TGAT 2525 CJMSLT_ST1_1312_1342_F TGGAAATGGCA 538 CJMSLT_ST1_1383_1417_R TTTCCCCGATC 1432 GCTAGAATAGT TAAATTTGGATAA AGCTAAAAT GCCATAGGAAA 2526 CJMSLT_ST1_2254_2286_F TGGGCCTAATG 582 CJMSLT_ST1_2352_2379_R TCCAAACGATC 996 GGCTTAATATC TGCATCACCATCA AATGAAAATTG AAAG 2527 CJMSLT_ST1_1380_1411_F TGCTTTCCTAT 534 CJMSLT_ST1_1486_1520_R TGCATGAAGCATA 1205 GGCTTATCCAA AAAACTGTATCAA ATTTAGATCG GTGCTTTTA 2528 CJMLST_ST1_3413_3437_F TTGTAAATGCC 692 CJMLST_ST1_3511_3542_R TGCTTGCTCAAAT 1257 GGTGCTTCAGA CATCATAAACAAT TCC TAAAGC 2529 CJMSLT_ST1_1130_1156_F TACGCGTCTTG 189 CJMSLT_ST1_1203_R TAGGATGAGCATT 920 AAGCGTTTCGTTA ATCAGGGAAAGAA TGA AGAATC 2530 CJMSLT_ST1_2840_2872_F TGGGGCTTTGC 591 CJMSLT_ST1_2940_2973_R TAGCGATTTCT 917 TTTATAGTTTT ACTCCTAGAGTTG TTACATTTAAG AAATTTCAGG 2531 CJMSLT_ST1_2058_2084_F TATTCAAGGTG 241 CJMSLT_ST1_2131_2162_R TTGGTTCTTACTT 1417 GTCCTTTGATG GTTTTGCATAAAC CATGT TTTCCA 2532 CJMSLT_ST1_553_585_F TCCTGATGCTC 344 CJMLST_ST1_655_685_R TATTGCTTTTTTT 942 AAAGTGCTTTT GCTATGCTTCTTG TTAGATCCTTT GACAT 2564 GTLA_NC002163- TCATGTTGAGC 299 GTLA_NC002163-1604930- TTTTGCTCATGAT 1443 1604930- TTAAACCTATA 1604529_352_380_R CTGCATGAAGCAT 1604529_306_338_F GAAGTAAAAGC AAA 2565 UNCA_NC002163- TCCCCCACGCT 322 UNCA_NC002163-112166- TCGACCTGGAGGA 1065 112166- TTAATTGTTTT 112647_146_171_R CGACGTAAAATCA 112647_80_113_F ATGATGATTTG CGACGTAAAATCA AG 2566 UNCA_NC002163- TAATGATGAAT 170 UNCA_NC002316-112166- TGGGATAACAT 1285 112166- TAGGTGCGGGT 112647_294_329_R TGGTTGGAATATA 112647_233_305_F TCTTT AGCAGAAACATC 2567 PGM_NC002163- TCTTGATACTT 414 PGM_NC002163-327773- TCCATCGCCAGTT 1012 327773- GTAATGTGGGC 328270_365_396_R TTTGCATAATCGC 328270_273_305_F GATAAATATGT TAAAAA 2568 TKT_NC002163- TTATGAAGCGT 661 TKT_NC002163-1569415- TCAAAACGCATTT 946 1569415- GTTCTTTAGCA 1569873_350_383_R TTACATCTTCGTT 1569873_255_284_F GGACTTCA AAAGGCTA 2570 GTLA_NC002163- TCGTCTTTTTG 381 GLTA_NC002163-1604930- TGTTCATGTTTAA 1347 1604930- ATTCTTTCCCT 1604529_109_142_R ATGATCAGGATAA 1604529_39_68_F GATAATGC AAAGCACT 2571 TKT_NC002163- TGATCTTAAAA 472 TKT_NC002163-1569415- TGCCATAGCAAAG 1214 1569415- ATTTCCGCCAA 1569903_139_162_R CCTACAGCATT 1569903_33_62_F CTTCATTC CCTACAGCATT 2572 TKT_NC002163- TAAGGTTTATT 164 TKT_NC002163-1569415- TACATCTCCTTCG 886 1569415- GTCTTTGTGGA 1569903_313_345_R ATAGAAATTTCAT 1569903_207_239_F GATGGGGATTT TGCTATC 2573 TKT_NC002163- TAGCCTTTAAC 213 TKT_NC002163-1569415- TAAGACAAGGTTT 865 1569415- GAAAATGTAAA 1569903_449_481_R TGTGGATTTTTTA 1569903_350_383_F AATGCGTTTTG GCTTGTT A 2574 TKT_NC002163- TTCAAAAACTC 665 TKT_NC002163-1569415- TTGCCATAGCAAA 1405 1569415- CAGGCCATCCT 1569903_139_163_R GCCTACAGCATT 1569903_60_92_F GAAATTTCAAC 2575 GTLA_NC002163- TCGTCTTTTTG 382 GLTA_NC002163-1604930- TGCCATTTCCATG 1216 1604930- ATTCTTTCCCT 1604529_139_168_R TACTCTTCTCTAA 1604529_39_70_F GATAATGCTC CATT 2576 GLYA_NC002163- TCAGCTATTTT 281 GLYA_NC002163-367572- ATTGCTTCTTACT 756 367572- TCCAGGTATCC 368079_476_508_R TGCTTAGCATAAA 368079_386_414_F AAGGTGG TTTTCCA 2577 GLYA_NC002163- TGGTGCGAGTG 611 GLYA_NC002163-367572- TGCTCACCTGCTA 1246 367572- CTTATGCTCGT 368079_242_270_R CAACAAGTCCAGC 368079_148_174_F ATTAT AAT 2578 GLYA_NC002163- TGTAAGCTCTA 622 GLYA_NC002163-367572- TTCCACCTTGGAT 1381 367572- CAACCCACAAA 368079_384_416_R ACCTGGAAAAATA 368079_298_327_F ACCTTACG GCTGAAT 2579 GLYA_NC002163- TGGTGGACATT 614 GLYA_NC002163-367572- TCAAGCTCTACAC 961 367572- TAACACATGGT 368079_52_81_R CATAAAAAAAGCT 368079_1_27_F GCAAA CTCA 2580 PGM_NC002163- TGAGCAATGGG 455 PGM_NC002163-327746- TTTGCTCTCCGCC 1438 327746- GCTTTGAAAGA 328270_356_379_R AAAGTTTCCAC 328270_254_285_F AAGAATTTTTA AAT 2581 PGM_NC002163- TGAAAAGGGTG 425 PGM_NC002163-327746- TGCCCCATTGCTC 1219 327746- AAGTAGCAAAT 328270_241_267_R TCATGATAGTAGT 328270_153_182_F GGAGATAG AGCTAC 2582 PGM_NC002163- TGGCCTAATGG 568 PGM_NC002163-327746- TGCACGCAAACGC 1200 327746- GCTTAATATCA 328270_79_102_R TTTACTTCAGC 328270_19_50_F ATGAAAATTG 2583 UNCA_NC002163- TAAGCATGCTG 160 UNCA_NC002163-112166- TGCCCTTTCTAAA 1220 112166- TGGCTTATCGT 112647_196_225_R AGTCTTGAGTGAA 112647_114_141_F GAAATG GATA 2584 UNCA_NC002163- TGCTTCGGATC 532 UBCA_NC002163-112166- TGCATGCTTACTC 1206 112166- CAGCAGCACTT 532 112647_88_123_R AAATCATCATAAA 112647_3_29_F CAATA CAATTAAAGC 2585 ASPA_NC002163- TTAATTTGCCA 652 ASPA_NC002163-96692- TGCAAAAGTAACG 1192 96692- AAAATGCAACC 97166_403_432_R GTTACATCTGCTC 97166_308_335_F AGGTAG CAAT 2586 ASPA_NC002163- TCGCGTTGCAA 370 ASPA_NC002163-966692- TCATGATAGAACT 991 96692- CAAAACTTTCT 97166_316_346_R ACCTGGTTGCATT 97166_228_258_F AAAGTATGT TTTGG 2587 GLNA_NC002163- TGGAATGATGA 547 GLNA_NC002163-658085- TGAGTTTGAACCA 1176 658085- TAAAGATTTCG 657609_340_371_R TTTCAGAGAGCGA 657609_244_275_F CAGATAGCTA ATATCTAC 2588 TKT_NC002163- TCGCTACAGGC 371 TKT_NC002163-1569415- TCCCCATCTCCGC 1020 1569415- CCTTTAGGACA 1569903_212_236_R AAAGACAATAAA 1569903_107_130_F CAGATAGCTA ATATCTAC 2589 TKT_NC002163- TGTTCTTTAGC 642 TKT_NC002163-1569415- TCCTTGTGCTTCA 1057 1569415- AGGACTTCACA 1569903_361_393_R AAACGCATTTTTA 1569903_265_296_F AACTTGATAA CATTTTC 2590 GLYA_NC002163- TGCCTATCTTT 505 GLYA_NC002163-367572- TCCTCTTGGGCCA 1047 367572- TTGCTGATATA 368095_317_340_R CGCAAAGTTTT 368095_214_246_F GCACATATTGC CGCAAAGTTTT 2591 GLYA_NC002163- TCCTTTGATGC 353 GLYA_NC002163-367572- TCTTGAGCATTGG 1141 367572- ATGTAATTGCT 368095_485_516_R TTCTTACTTGTTT 368095_415_444_F GCAAAAGC TGCATA 2592 PGM_NC002163_21_54_F TCCTAATGGAC 332 PGM_NC002163_116_142_R TCAAACGATCCGC 949 TTAATATCAAT ATCACCATCAAAA GAAAATTGTGG G G 2593 PGM_NC002163_149_176_F TAGATGAAAAA 207 PGM_NC002163_247_277_R TCCCCTTTAAAGC 1023 GGCGAAGTGGC ACCATTACTCATT TAATGG ATAGT 2594 GLNA_NC002163- TGTCCAAGAAG 633 GLNA_NC002163-658085- TCAAAAACAAAGA 658085- CATAGCAAAAA 657609_148_179_R ATTCATTTTCTGG 657609_79_106_F AAGCAA TCCAAA 2595 ASPA_NC2163- TCCTGTTATTC 347 ASPA_NC002163-96685- TCAAGCTATATGC 960 96685- CTGAAGTAGTT 97196_467_497_R TACAACTGGTTCA 97196_367_402_F AATCAAGTTTG AAAAC TTA 2596 ASPA_NC002163- TGCCGTAATGA 502 ASPA_NC002163-96685- TACAACCTTCGGA 880 96685- TAGGTGAAGAT 97196_95_127_R TAATCAGGATGAG 97196_1_33_F ATACAAAGAGT AATTAAT 2597 ASPA_NC002163- TGGAACAGGAA 540 ASPA_NC002163-96685- TAAGCTCCCGTAT 872 96685- TTAATTCTCAT 97196_185_210_R CTTGAGTCGCCTC 97196_85_117_F CCTGATTATCC 2598 PGM_NC002163- TGGCAGCTAGA 563 PGM_NC002163-327746- TCACGATCTAAAT 975 327746- ATAGTAGCTAA 328270_230_261_R TTGGATAAGCCAT 328270_165_195_F AATCCCTAC AGGAAA 2599 PGM_NC002163- TGGGTCGTGGT 593 PGM_NC002163-327746- TTTTGCTCATGAT 1443 327746- TTTACAGAAAA 328270_353_381_R CTGCATGAAGCAT 328270_252_286_F TTTCTTATATA AAA 2600 PGM_NC002163- TGGGATGAAAA 577 PGM_NC002163-327746- TGATAAAAAGCAC 1178 327746- AGCGTTCTTTT 328270_95_123_R TAAGCGATGAAAC 328270_1_30_F ATCCATGA AGC 2601 PGM_NC002163- TAAACACGGCT 146 PGM_NC002163-327746- TCAAGTGCTTTTA 963 327746- TTCCTATGGCT 328270_314_345_R CTTCTATAGGTTT 328270_220_250_F TATCCAAAT AAGCTC 2602 UNCA_NC002163- TGTAGCTTATC 628 UNCA_NC002163-112166- TGCTTGCTCTTTC 1258 112166- GCGAAATGTCT 112647_199_229_R AAGCAGTCTTGAA 112647_123_152_F TTGATTTT TGAAG 2603 UBCA_NC002163- TCCAGATGGAC 313 UNCA_NC002163-112166- TCCGAAACTTGTT 1031 112166- AAATTTTCTTA 112647_430_461_R TGTAGCTTTAATT 112647_333_365_F GAAACTGATTT TGAGC 2734 GYRA_AY291534_237_264_F TCACCCTCATG 265 GYRA_AY291534_268_288_R TTGCGCCATACGT 1407 GTGATTCAGCT ACCATCGT GTTTAT 2735 GYRA_AY291534_224_252_F TAATCGGTAAG 167 GYRA_AY291534_256_285_R TGCCATACGTACC 1213 TATCACCCTCA ATCGTTTCATAAA TGGTGAT CAGC 2736 GYRA_AY291534_170_198_F TAGGAATTACG 221 GYRA_AY291534_268_288_R TTGCGCCATACGT 1407 GCTGATAAAGC ACCATCGT GTATAAA 2737 GYRA_AY291534_224_252_F TAATCGGTAAG 167 GYRA_AY291534_319_346_R TATCGACAGATCC 935 ATCACCCTCAT AAAGTTACCATGC GGTGAT CC 2738 GYRA_NC002953-7005- TAAGGTATGAC 163 GYRA_NC002953-7005- TCTTGAGCCATAC 1142 9668_166_195_F ACCGGATAAAT 9668_265_287_R GTACCATTGC CATATAAA GTACCATTGC 2739 GYRA_NC002953-7005- TAATGGGTAAA 171 GYRA_NC002953-7005- TATCCATTGAACC 933 9668_221_249_F TATCACCCTCA 9668_316_343_R AAAGTTACCTTGG TGGTGAC CC 2740 GYRA_NC002953-7005- TAATGGGTAAA 171 GYRA_NC002953-7005- TAGCCATACGTAC 912 9668_221_249_F TATCACCCTCA 9668_253_283_R CATTGCTTCATAA TGGTGAC AATAGA 2741 GYRA_NC002953-7005- TCACCCTCATG 264 GYRA_NC002953-7005- TCTTGAGCCATAC 1142 9668_234_261_F GTGACTCATCT 9668_265_287_R GTACCATTGC ATTTAT 2842 CAPC_AF188935- TGGGATTATTG 578 CAPC_AF188935-56074- TGGTAACCCTTGT 1299 56074- TTATCCTGTTA 55628_348_378_R CTTTGAATTGTAT 55628_271_304_F TGCCATTTGAG TTGCA A 2843 CAPC_AF188935- TGATTATTGTT 476 CAPC_AF188935-56074- TGTAACCCTTGTC 1344 56074- ATCCTGTTATG 55628_349_377P_R TTTGAATpTpGTA 55628_273_303P_F CpCpATpTpTp TpTpTpGC GAG 2844 CAPC_AF188935- TCCGTTGATTA 331 CAPC_AF188935-56074- TGTTAATGGTAAC 1344 56074- TTGTTATCCTG 55628_349_384_R CCTTGTCTTTGAA 55628_268_303_F TTATGCCATTT TTGTATTTGC GAG 2845 CAPC_AF188935- TCCGTTGATTA 331 CAPC_AF188935-56074- TAACCCTTGTCTT 860 56074- TTGTTATCCTG 55628_337_375_R TGAATTGTATTTG 55628_268_303_F TTATGCCATTT CAATTAATCCTGG GAG 2846 PARC_X95819_33_58_F TCAAAAAAAT 302 PARC_X95819_121_153_R TAAAGGATAGCGG 852 CAGCGCGTACA TAACTAAATGGCT GTGG GAGCCAT 2847 PARC_X95819_65_92_F TACTTGGTAAA 199 PARC_X95819_157_178_R TACCCCAGTTCCC 889 TACCACCCACA CTGACCTTC TGGTGA 2848 PARC_X95819_69_93_F TGGTAAATACC 596 PARC_X95819_97_128_R TGAGCCATGAGTA 1169 ACCCACACATG CCATGGCTTCATA GTGAC ACATGC 2849 PARC_NC003997- TTCCGTAAGTC 668 PARC_NC003997-3362578- TCCAAGTTTGACT 1001 3362578- GGCTAAAACAG 3365001_256_283_R TAAACGTACCATC 3365001_181_205_F TCG GC 2850 PARC_NC003997- TGTAACTATCA 621 PARC_NC003997-3362578- TCGTCAACACTAC 1099 3362578- CCCGCACGGTG 3365001_304_335_R CATTATTACCATG 3365001_217_240_F AT CATCTC 2851 PARC_NC003997- TGTAACTATCA 621 PARC_NC003997-3362578- TGACTTAAACGTA 1162 3362578- CCCGCACGGTG 3365001_244_275_R CCATCGCTTCATA 3365001_217_240_F AT TCATCTC 2852 GYRA_AY642140_1_24_F TAAATCTGCCC 150 GYRA_AY642140_71_100_R TGCTAAAGTCTTG 1242 CGTGTCGTTGG AGCCATACGAACA TGAC ATGG 2853 GYRA_AY642140_26_54_F TAATCGGTAAA 166 GYRA_AY642140_121_146_R TCGATCGAACCGA 1069 TATCACCCGCA AGTTACCCTGACC TGGTGAC 2854 GYRA_AY642140_26_54_F TAATCGGTAAA 166 GYRA_AY642140_58_89_R TGAGCCATACGAA 1168 TATCACCCGCA CAATGGTTTCATA TGGTGAC AACAGC 2860 CYA_AF065404_1348_1379_F TCCAACGAAGT 305 CYA_AF065404_1448_1472_R TCAGCTGTTAACG 983 ACAATACAAGA GCTTCAAGACCC CAAAAGAAGG 2861 FEF_BA_AF065404_751_781_F TCGAAAGCTTT 354 LEF_BA_AF065404_843_881_R TCTTTAAGTTCTT 1144 TGCATATTATA CCAAGGATAGATT TCGAGCCAC TATTTCTTGTTCG 2862 LEF_BA_AF065404_762_788_F TGCATATTATA 498 LEF_BA_AF065404_843_881_R TCTTTAAGTTCTT 1144 TCGAGCCACAG CCAAGGATAGATT CATCG TATTTCTTGTTCG 2917 MUTS_AY698802_106_125_F TCCGCTGAATC 326 MUTS_AY698802_172_193_R TGCGGTCTGGCGC 1237 TGTCGCCGC ATATAGGTA 2918 MUTS_AY698802_172_192_F TACCTATATGC 187 MUTS_AY698802_228_252_R TCAATCTCGACTT 965 GCCAGACCGC TTTGTGCCGGTA 2919 MUTS_AY698802_228_252_F TACCGGCGCAA 186 MUTS_AY698802_314_342_R TCGGTTTCAGTCA 1097 AAAGTCGAGAT TCTCCACCATAAA TGG GGT 2920 MUTS_AY698802_315_342_F TCTTTATGGTG 419 MUTS_AY698802_413_433_R TGCCAGCGACAGA 1210 GAGATGACTGAAA CCATCGTA CCGA 2921 MUTS_AY698802_394_411_F TGGGCGTGGAA 585 MUTS_AY698802_497_519_R TCCGGTAACTGGG 1040 CGTCCAC TCAGCTCGAA 2922 AB_MLST-11- TGGGcGATGCT 583 AB_MLST-11- TAGTATCACCACG 923 OIF007_991_1018_F GCgAAATGGTT OIF007_1110_1137_R TACACCCGGATCA AAAAGA GT 2927 GAPA_NC002505_694_721_F TCAATGAACGA 259 GAPA_NC_002505_29_58_R_1 TCCTTTATGCAAC 1060 CCAACAAGTGA TTGGTATCAACAG TTGATG GAAT 2928 GAPA_NC002505_694_721_2_F TCGATGAACGA 361 GAPA_NC002505_769_798_2_R TCCTTTATGCAAC 1061 CCAACAAGTGA TTGGTATCAACCG TTGATG GAAT 2929 GAPA_NC002505_694_721_2_F TCGATGAACGA 361 GAPA_NC002505_769_798_3_R TCCTTTATGCAAC 1059 CCAACAAGTGA TTAGTATCAACCG TTGATG GAAT 2932 INFB_EC_1364_1394_F TTGCTCGTGGT 688 INFB_EC_1439_1468_R TTGCTGCTTTCGC 1410 GCACAAGTAA ATGGTTAATCGCT CGGATATTAC TCAA 2933 INFB_EC_1364_1394_2_F TTGCTCGTGGT 689 INFB_EC_1439_1468_R TTGCTGCTTTCGC 1410 GCAIAAGTAA ATGGTTAATCGCT CGGATATIAC TCAA 2934 INFB_EC_80_110_F TTGCCCGCGGT 685 INFB_EC_1439_1468_R TTGCTGCTTTCGC 1410 GCGGAAGTAAC ATGGTTAATCGCT CGATATTAC TCAA 2949 ACS_NC002516- TCGGCGCCTGC 376 ACS_NC002516-970624- TGGACCACGCCGA 1265 970624- CTGATGA 971013_364_383_R AGAACGG 2950 ARO_NC002516_26883- TCACCGTGCCG 267 ARO_NC002516-26883- TGTGTTGTCGCCG 1341 27380_4_26_F TTCAAGGAAGA 27380_111_128_R CGCAG G 2951 ARO_NC002516-26883- TTTCGAAGGGC 705 ARO_NC002516-26883- TCCTTGGCATACA 1056 27380_356_377_F CTTTCGACCTG 27380_459_484_R TCATGTCGTAGCA 2952 GUA_NC002516- TGGACTCCTCG 551 GUA_NC002516-4226546- TCGGCGAACATGG 1091 4226546- GTGGTCGC 4226174_127_146_R CCATCAC 2953 GUA_NC002516- TGACCAGGTGA 448 GUA_NC002516-4226546- TGCTTCTCTTCCG 1256 4226546- TGGCCATGTTC 4226174_214_233_R GGTCGGC 4226174_120_142_F G 2954 GUA_NC002516- TTTTGAAGGTG 710 GUA_NC002516-4226546- TGCTTGGTGGCTT 1259 4226546- ATCCGTGCCAA 4226174_265_287_R CTTCGTCGAA 4226174_155_178_F CG 2955 GUA_NC002516- TTCCTCGGCCG 670 GUA_NC002516-4226546- TGCGAGGAACTTC 1229 4226546- CCTGGC 4226174_288_309_R ACGTCCTGC 4226174_190_206_F 2956 GUA_NC002516- TCGGCCGCACC 374 GUA_NC002516-4226546- TCGTGGGCCTTGC 1111 4226546- TTCATCGAAGT 4226174_355_371_R CGGT 2957 MUT_NC002516- TGGAAGTCATC 545 MUT_NC002516-5551158- TCACGGGCCAGCT 978 5551158- AAGCGCCTGGC 5550717_99_116_R CGTCT 5550717_5_26_F AAGCGCCTGGC 2958 MUT_NC002516- TCGAGCAGGC 358 MUT_NC002516-5551158- TCACCATGCGCCC 971 5551158- GCTGCCG 5550717_256_277_R GTTCACATA 5550717_5_26_F 2959 NUO_NC002516- TCAACCTCGGC 249 NUO_NC002516-2984589- TCGGTGGTGGTAG 1095 2984589- CCGAACCA 2984954_97_117_R CCGATCTC 2960 NUO_NC002516- TACTCTCGGTG 195 NUO_NC002516-2984589- TTCAGGTACAGCA 1376 2984589- GAGAAGCTCGC 2984954_301_326_R GGTGGTTCAGGAT 2961 PPS_NC002516- TCCACGGTCAT 311 PPS_NC002516-1915014- TCCATTTCCGACA 1014 1915014- GGAGCGCTA 1915383_140_165_R CGTCGTTGATCAC 1915383_44_63_P 3962 PPS_NC002516- TCGCCATCGTC 365 PPS_NC002516-1915014- TCCTGGCCATCCT 1052 1915014- ACCAACCG 1915383_341_360_R GCAGGAT 1915383_240_258_F 2963 TRP_NC002516- TGCTGGTACGG 527 TRP_NC002516-671831- TCGATCTCCTTG 1071 671831- GTCGAGGA 672273_131_150_R GCGTCCGA 672273_24_42_F 2964 TRP_NC002516- TGCACATCGTG 490 TRP_NC002516-671831- TGATCTCCATGGC 1182 671831- TCCAACGTCAC 672273_362_383_R GCGGATCTT 672273_261_282_F 2972 AB_MLST-11- TGGGIGATGCT 592 AB_MLST-11- TAGTATCACCACG 924 OIF007_1007_1034_F GCIAAATGGTT OIF007_1126_1153_R TACICCIGGATCA AAAAGA GT 2993 OMPU_NC002505- TTCCCACCGAT 667 OMPU_NC002505_544_567_R TCGGTCAGCAAAA 1094 674828- ATCATGGCTTA CGGTAGCTTGC 675880_428_455_F 2994 GAPA_NC002505- TCCTCAATGAA 335 GAPA_NC002505-506780- TTTTCCCTTTATG 1442 506780 CGAICAACAAG 507937_769_802_R CAACTTAGTATCA 507937_691_721_F TGATTGATG ACIGGAAT 2995 GAPA_NC002505- TCCTCIATGAA 339 GAPA_NC002505-506780- TCCATACCTTTAT 1008 506780- ACGAICAACAA 507937_769_803_R GCAACTTIGTAT 507937_691_721_2_F GTGATTGATG CAACIGGAAT 2996 GAPA_NC002505- TCCTCGATGAA 396 GAPA_NC002505-506780- TCGGAAATATTCT 1085 506780- CCGACCAACAA 507937_785_817_R TTCAATACCTT 507937_692_721_F GTGATTGATTG TATGCAACT 2997 GAPA_NC002505- TCCTCGATGAA 337 GAPA_NC002505-506780- TCGGAAATATTCT 1085 506780- CGAICAACAAG 507937_785_817_R TTCAATACCTTTA 507937_691_721_3_F TIATTGATG TGCAACT 2998 GAPA_NC002505- TCCTCAATGAA 336 GAPA_NC002505-506780- TCGGAAATATTCT 1087 506780- TGATCAACAAG 507937_784_817_R TTCAATICCTTTI 507937_691_721_4_F TGATTGATG TGCAACTT 2999 GAPA_NC002505- TCCTCIATGAA 340 GAPA_NC002505-506780- TCGGAAATATTCT 1086 506780- IGAICAACAAG 507937_784_817_2_R TTCAATACCTTTA 507937_691_721_5_F TIATTGATG TGCAACTT 3000 GAPA_NC002505- TCCTCGATGAA 338 GAPA_NC002505-506780- TTTCAATACCTTT 1430 506780- TGAICAACAAC 507937_769_805_R GCAACTTIGTATC 507937_691_721_6_F AAGTIATTGAT AACIGGAAT G 3001 CTXB_NC002505- TCAGCATATGC 275 CTXB_NC002505-1566967- TCCCGGCTAGAGA 1026 1566967- ACATGGAACAC 1567341_139_163_R TTCTGTATACGA 1567341_46_71_F CTCA TTCTGTATACGA 3002 CTXB_NC002505- TCAGCATATGC 274 CTXB_NC002505-1566967- TCCGGCTAGAGAT 1038 1566967- ACATGGAACAC 1567341_132_162_R TCTGTATACGAAA 1567341_46_70_F CTC ATATC 3003 CTXB_NC002505- TCAGCATATGC 274 CTXB_NC002505-1566967- TGCCGTATACGAA 1225 1566967- ACATGGAACAC 1567341_118_150_R AATATCTTATCAT 1567341_46_70_F CTC TTAGCGT 3004 TUFB_NC002758- TACAGGCCGTG 180 TUFB_NC002758-615038- TCAGCGTAGTCTA 982 615038- TTGAACGTGG 61622_778_809_R ATAATTTACGGAA 616222_684_704_F CATTTC 3005 TUFB_NC002758- TGCCGTGTTGA 503 TUFB_NC0027858-615038- TGCTTCAGCGTAG 1255 615038- ACGTGGTCAAA 616222_783_813_R TCTAATAATTTAC 616222_688_710_F T GGAAC 3006 TUFB_NC0027858- TGTGGTCAAAT 638 TUFB_NC002758-615038- TGCGTAGTCTAAT 1238 615038- CAAAGTTGGTG 616222_778_807_R AATTTACGGAACA 616222_700_726_F AAGA TTTC 3007 TUFB_NC002758- TGGTCAAATCA 607 TUFB_NC002758-615038- TGCGTAGTCTAAT 1238 615038- AAGTTGGTGAAG 616222_778_807_R AATTTACGGAACA 616222_702_726_F AA TTTC 3008 TUFB_NC002758- TGAACGTGGTC 431 TUFB_NC002758-615038- TCACCAGCTTCAG 970 615038- AAATCAAAGTT 616222_785_818_R CGTAGTCTAATAA 616222_696_726_F GGTGAAGAA TTTACGGA 3009 TUFB_NC002758- TCGTGTTGAAC 386 TUFB_NC002758-615038- TCTTCAGCGCGTA 1134 615038- GTGGTCAAATC 616222_778_812_R GTCTAATAATTTA 616222_690_716_F AAAGT CGGAACATTTC 3010 MECI-R-NC003923- TCACATATCGT 261 MECI-R_NC003923-41798- TGTGATATGGAGG 1332 41798-41609_36_59_F GAGCAATGAAC 41609_89_112_R TGTAGAAGGTG TG 3011 MECI-R_NC003923- TGGGCGTGAGC 584 MECI-R_NC003923-41798- TGGGATGGAGGTG 1287 41798-41609_40_66_F AATGAACTGAT 41609_81_110_R TAGAAGGTGTTAT TATAC CATC 3012 MECI-R_NC003923- TGGACACATAT 549 MECI-R_NC003923-41798- TGGGATGGAGGTG 1286 41798- CGTGAGCAATG 41609_81_110_R TAGAAAGGTGTTA 41609_33_60_2_F AACTGA TCATC 3013 MECI-R_NC003923- TGGGTTTACAC 595 MECI-R_NC003923-41798- TGGGGATATGGAG 1290 41798-41609_29_60_F ATATCGTGAGC 41609_81_113_R TGTAGAAGGTGTT AATGAACTGA ATCATC 3014 MUPR_X75439_2409_2513_F TGGGCTCTTTC 587 MUPR_X75439_2548_2570_R TCTGGCTGCGGAA 1130 TCGCTTAAACA GTGAAATCGT CCT 3015 MUPR_X75439_2482_2510_F TGGGCTCTTTC 586 MUPR_X75439_2547_2568_R TGGCTGCGGAAGT 1281 TCGCTTAAACA GAAATCGTA CC 3016 MUPR_X75439_2482_2510_F TAGATAATTGG 205 MUPR_X75439_2551_2573_R TAATCTGGCTGCG 876 GCTCTTTCTCG GAAGTGAAAT CTTAAAC 3017 MUPR_X75439_2490_2514_F TGGGCTCTTTC 587 MUPR_X75439_2549_2573_R TAATCTGGCTGCG 877 TCGCTTAAACA GAAGTGAAATCG CCT 3018 MUPR_X75439_2482_2510_F TAGATAATTGG 205 MUPR_X75439_2559_2589_R TGGTATATTCGTT 1303 GCTCTTTCTCG AATTAATCTGGCT CTTAAAC GCGGA 3019 MUPR_X75439_2490_2514_F TGGGCTCTTTC 587 MUPR_X75439_2554_2581_R TCGTTAATTAATC 1112 GCTTAAACACC TGGCTGCGGAAGT T GA 3020 AROE_NC003923- TGATGGCAAGT 474 AROE_NC003923-1674726- TAAGCAATACCTT 1378 1674726- GGATAGGGTAT 1674277_309_335_R TACTTGCACCACC 1674277_204_232_F AATACAG ACCT 3021 AROE_NC003923- TGGCGAGTGGA 570 AROE_NC003923-1674726- TTCATAAGCAATA 1378 1674726- TAGGGTATAAT 1674277_311_339_R CCCTTTACTTGCA 1674277_207_232_F ACAG CCAC 3022 AROE_NC003923- TGGCpAAGTpG 572 AROE_NC003923-1674726- TAAGCAATACCpT 867 1674726- GATpAGGGTpA 1674277_311_335P_R pTpTpACTpTpGC 1674277_207_232P_F TpAATpACpAG pACpCpAC 3023 ARCC_NC003923- TCTGAAATGAA 398 ARCC_NC003923-2725050- TCTTCTTCTTTCG 1137 2725050- TAGTGATAGAA 2724595_214_245_R TATAAAAAGGACC 2724595_124_155_F CTGTAGGCAC AATTGG 3024 ARCC_NC003923- TGAATAGTGAT 437 ARCC_NC003923-2725050- TCTTCTTTTCGTAT 1139 2725050- AGAACTGTAGG 2724595_212_242_R AAAAAGGACCAAT 2724595_131_161_F CACAATCGT TGGTT 3025 ARCC_NC003923- TGAATAGTGAT 437 ARCC_NC003923-2725050- TGCGCTAATTCTT 1232 2725050- AGAACTGTAGG 2724595_232_260_R CAACTTCTTCTTT 2724595_131_161_F CACAATCGT CGT 3026 PTA_NC003923- TACAATGCTTG 177 PTA_NC003923-628885- TGTTCTTGATACA 1350 628885- TTTATGCTGGTA 629355_322_351_R CCTGGTTTCGTTT 629355_231_259_F AAGCAG TGAT 3027 PTA_NC003923- TACAATGCTTG 177 PTA_NC003923-628885- TGGTACACCTGGT 1301 62885- TTTATGCTGGT 629355_314_345_R TTCGTTTTGATGA 629355_231_259_F AAAGCAG TTTGTA 3028 PTA_NC003923- TCTTGTTTATG 418 PTA_NC003923-628885- TGTTCTTGATACA 1350 628885- CTGGTAAAAGC 629355_322_351_R CCTGGTTTCGTTT 629355_237_263_F AGATGG TGAT

Primer pair name codes and reference sequences are shown in Table 3. The primer name code typically represents the gene to which the given primer pair is targeted. The primer pair name may include specific coordinates with respect to a reference sequence defined by an extraction of a section of sequence or defined by a GenBank gi number, or the corresponding complementary sequence of the extraction, or the entire GenBank gi number as indicated by the label “no extraction.” Where “no extraction” is indicated for a reference sequence, the coordinates of a primer pair named to the reference sequence are with respect to the GenBank gi listing. Gene abbreviations are shown in bold type in the “Gene Name” column.

To determine the exact primer hybridization coordinates of a given pair of primers on a given bioagent nucleic acid sequence and to determine the sequences, molecular masses and base compositions of an amplification product to be obtained upon amplification of nucleic acid of a known bioagent with known sequence information in the region of interest with a given pair of primers, one with ordinary skill in bioinformatics is capable of obtaining alignments of the primers of the present invention with the GenBank gi number of the relevant nucleic acid sequence of the known bioagent. For example, the reference sequence GenBank gi numbers (Table 3) provide the identities of the sequences which can be obtained from GenBank. Alignments can be done using a bioinformatics tool such as BLASTn provided to the public by NCBI (Bethesda, Md.). Alternatively, a relevant GenBank sequence may be downloaded and imported into custom programmed or commercially available bioinformatics programs wherein the alignment can be carried out to determine the primer hybridization coordinates and the sequences, molecular masses and base compositions of the amplification product. For example, to obtain the hybridization coordinates of primer pair number 2095 (SEQ ID NOs: 456:1261), First the forward primer (SEQ ID NO: 456) is subjected to a BLASTn search on the publicly available NCBI BLAST website. “RefSeq_Genomic” is chosen as the BLAST database since the gi numbers refer to genomic sequences. The BLAST query is then performed. Among the top results returned is a match to GenBank gi number 21281729 (Accession Number NC_(—)003923). The result shown below, indicates that the forward primer hybridizes to positions 1530282.1530307 of the genomic sequence of Staphylococcus aureus subsp. aureus MW2 (represented by gi number 21281729).

Staphylococcus aureus subsp. aureus MW2, complete genome Length=2820462

Features in this part of subject sequence:

-   -   Panton-Valentine leukocidin chain F precursor         Score=52.0 bits (26), Expect=2e-05         Identities=26/26 (100%), Gaps=0/26 (0%)

Strand=Plus/Plus Query       1 TGAGCTGCATCAACTGTATTGGATAG      26 |||||||||||||||||||||||||| Sbjct 1530282 TGAGCTGCATCAACTGTATTGGATAG 1530307

The hybridization coordinates of the reverse primer (SEQ ID NO: 1261) can be determined in a similar manner and thus, the bioagent identifying amplicon can be defined in terms of genomic coordinates. The query/subject arrangement of the result would be presented in Strand=Plus/Minus format because the reverse strand hybridizes to the reverse complement of the genomic sequence. The preceding sequence analyses are well known to one with ordinary skill in bioinformatics and thus, Table 3 contains sufficient information to determine the primer hybridization coordinates of any of the primers of Table 2 to the applicable reference sequences described therein. TABLE 3 Primer Name Codes and Reference Sequence Reference GenBank gi Primer name code Gene Name Organism number 16S_EC 16S rRNA (16S ribosomal RNA gene) Escherichia coli 16127994 23S_EC 23S rRNA (23S ribosomal RNA gene) Escherichia coli 16127994 CAPC_BA capC (capsule biosynthesis gene) Bacillus anthracis 6470151 CYA_BA cya (cyclic AMP gene) Bacillus anthracis 4894216 DNAK_EC dnaK (chaperone dnaK gene) Escherichia coli 16127994 GROL_EC groL (chaperonin groL) Escherichia coli 16127994 HFLB_EC hflb (cell division protein peptidase Escherichia coli 16127994 ftsH) INFB_EC infB (protein chain initiation factor Escherichia coli 16127994 infB gene) LEF_BA lef (lethal factor) Bacillus anthracis 21392688 PAG_BA pag (protective antigen) Bacillus anthracis 21392688 RPLB_EC rplB (50S ribosomal protein L2) Escherichia coli 16127994 RPOB_EC rpoB (DNA-directed RNA polymerase beta Escherichia coli 6127994 chain) RPOC_EC rpoC (DNA-directed RNA polymerase Escherichia coli 16127994 beta' chain) SP101ET_SPET_11 Artificial Sequence Concatenation Artificial 15674250 comprising: Sequence* - gki (glucose kinase) partial gene gtr (glutamine transporter protein) sequences of murI (glutamate racemase) Streptococcus mutS (DNA mismatch repair protein) pyogenes xpt (xanthine phosphoribosyl transferase) yqiL (acetyl-CoA-acetyl transferase) tkt (transketolase) SSPE_BA sspE (small acid-soluble spore Bacillus anthracis 30253828 protein) TUFB_EC tufB (Elongation factor Tu) Escherichia coli 16127994 VALS_EC valS (Valyl-tRNA synthetase) Escherichia coli 16127994 ASPS_EC aspS (Aspartyl-tRNA synthetase) Escherichia coli 16127994 CAF1_AF053947 caf1 (capsular protein caf1) Yersinia pestis 2996286 INV_U22457 inv (invasin) Yersinia pestis 1256565 LL_NC003143 Y. pestis specific chromosomal genes - Yersinia pestis 16120353 difference region BONTA_X52066 BoNT/A (neurotoxin type A) Clostridium 40381 botulinum MECA_Y14051 mecA methicillin resistance gene Staphylococcus 2791983 aureus TRPE_AY094355 trpE (anthranilate synthase (large Acinetobacter 20853695 component)) baumanii RECA_AF251469 recA (recombinase A) Acinetobacter 9965210 baumanii GYRA_AF100557 gyrA (DNA gyrase subunit A) Acinetobacter 4240540 baumanii GYRB_AB008700 gyrB (DNA gyrase subunit B) Acinetobacter 4514436 baumanii WAAA_Z96925 waaA (3-deoxy-D-manno-octulosonic-acid Acinetobacter 2765828 transferase) baumanii CJST_CJ Artificial Sequence Concatenation Artificial 15791399 comprising: Sequence* - tkt (transketolase) partial gene glyA (serine hydroxymethyltransferase) sequences of gltA (citrate synthase) Campylobacter aspA (aspartate ammonia lyase) jejuni glnA (glutamine synthase) pgm (phosphoglycerate mutase) uncA (ATP synthetase alpha chain) RNASEP_BDP RNase P (ribonuclease P) Bordetella 33591275 pertussis RNASEP_BKM RNase P (ribonuclease P) Burkholderia 53723370 mallei RNASEP_BS RNase P (ribonuclease P) Bacillus subtilis 16077068 RNASEP_CLB RNase P (ribonuclease P) Clostridium 18308982 perfringens RNASEP_EC RNase P (ribonuclease P) Escherichia coli 16127994 RNASEP_RKP RNase P (ribonuclease P) Rickettsia 15603881 prowazekii RNASEP_SA RNase P (ribonuclease P) Staphylococcus 15922990 aureus RNASEP_VBC RNase P (ribonuclease P) Vibrio cholerae 15640032 ICD_CXB icd (isocitrate dehydrogenase) Coxiella burnetii 29732244 IS1111A multi-locus IS1111A insertion element Acinetobacter 29732244 baumannii OMPA_AY485227 ompA (outer membrane protein A) Rickettsia 40287451 prowazekii OMPB_RKP ompB (outer membrane protein B) Rickettsia 15603881 prowazekii GLTA_RKP gltA (citrate synthase) Vibrio cholerae 15603881 TOXR_VBC toxR (transcription regulator toxR) Francisella 15640032 tularensis ASD_FRT asd (Aspartate semialdehyde Francisella 56707187 dehydrogenase) tularensis GALE_FRT galE (UDP-glucose 4-epimerase) Shigella flexneri 56707187 IPAH_SGF ipaH (invasion plasmid antigen) Campylobacter 30061571 jejuni HUPB_CJ hupB (DNA-binding protein Hu-beta) Coxiella burnetii 15791399 AB_MLST Artificial Sequence Concatenation Artificial Sequenced comprising: Sequence* - in-house trpE (anthranilate synthase component partial gene (SEQ ID I)) sequences of NO: 1444) adk (adenylate kinase) Acinetobacter mutY (adenine glycosylase) baumannii fumC (fumarate hydratase) efp (elongation factor p) ppa (pyrophosphate phospho- hydratase MUPR_X75439 mupR (mupriocin resistance gene) Staphylococcus 438226 aureus PARC_X95819 parC (topoisomerase IV) Acinetobacter 1212748 baumannii SED_M28521 sed (enterotoxin D) Staphylococcus 1492109 aureus PLA_AF053945 pla (plasminogen activator) Yersinia pestis 2996216 SEJ_AF053140 sej (enterotoxin J) Staphylococcus 3372540 aureus GYRA_NC000912 gyrA (DNA gyrase subunit A) Mycoplasma 13507739 pneumoniae ACS_NC002516 acsA (Acetyl CoA Synthase) Pseudomonas 15595198 aeruginosa ARO_NC002516 aroE (shikimate 5-dehydrogenase Pseudomonas 15595198 aeruginosa GUA_NC002516 guaA (GMP synthase) Pseudomonas 15595198 aeruginosa MUT_NC002516 mutL (DNA mismatch repair protein) Pseudomonas 15595198 aeruginosa NUO_NC002516 nuoD (NADH dehydrogenase I chain C, D) Pseudomonas 15595198 aeruginosa PPS_NC002516 ppsA (Phosphoenolpyruvate synthase) Pseudomonas 15595198 aeruginosa TRP_NC002516 trpE (Anthranilate synthetase Pseudomonas 15595198 component I) aeruginosa OMP2_NC000117 ompB (outer membrane protein B) Chlamydia 15604717 trachomatis OMPA_NC000117 ompA (outer membrane protein B) Chlamydia 15604717 trachomatis GYRA_NC000117 gyrA (DNA gyrase subunit A) Chlamydia 15604717 trachomatis CTXA_NC002505 ctxA (Cholera toxin A subunit) Vibrio cholerae 15640032 CTXB_NC002505 ctxB (Cholera toxin B subunit) Vibrio cholerae 15640032 FUR_NC002505 fur (ferric uptake regulator protein) Vibrio cholerae 15640032 GAPA_NC_002505 gapA (glyceraldehyde-3-phosphate Vibrio cholerae 15640032 dehydrogenase) GYRB_NC002505 gyrB (DNA gyrase subunit B) Vibrio cholerae 15640032 OMPU_NC002505 ompU (outer membrane protein) Vibrio cholerae 15640032 TCPA_NC002505 tcpA (toxin-coregulated pilus) Vibrio cholerae 15640032 ASPA_NC002163 aspA (aspartate ammonia lyase) Campylobacter 15791399 jejuni GLNA_NC002163 glnA (glutamine synthetase) Campylobacter 15791399 jejuni GLTA_NC002163 gltA (glutamate synthase) Campylobacter 15791399 jejuni GLYA_NC002163 glyA (serine hydroxymethyltransferase) Campylobacter 15791399 jejuni PGM_NC002163 pgm (phosphoglyceromutase) Campylobacter 15791399 jejuni TKT_NC002163 tkt (transketolase) Campylobacter 15791399 jejuni UNCA_NC002163 uncA (ATP synthetase alpha chain) Campylobacter 15791399 jejuni AGR-III_NC003923 agr-III (accessory gene regulator-III) Staphylococcus 21281729 aureus ARCC_NC003923 arcC (carbamate kinase) Staphylococcus 21281729 aureus AROE_NC003923 aroE (shikimate 5-dehydrogenase Staphylococcus 21281729 aureus BSA-A_NC003923 bsa-a (glutathione peroxidase) Staphylococcus 21281729 aureus BSA-B_NC003923 bsa-b (epidermin biosynthesis protein Staphylococcus 21281729 EpiB) aureus GLPF_NC003923 glpF (glycerol transporter) Staphylococcus 21281729 aureus GMK_NC003923 gmk (guanylate kinase) Staphylococcus 21281729 aureus MECI-R_NC003923 mecR1 (truncated methicillin Staphylococcus 21281729 resistance protein) aureus PTA_NC003923 pta (phosphate acetyltransferase) Staphylococcus 21281729 aureus PVLUK_NC003923 pvluk (Panton-Valentine leukocidin Staphylococcus 21281729 chain F precursor) aureus SA442_NC003923 sa442 gene Staphylococcus 21281729 aureus SEA_NC003923 sea (staphylococcal enterotoxin A Staphylococcus 21281729 precursor) aureus SEC_NC003923 sec4 (enterotoxin type C precursor) Staphylococcus 21281729 aureus TPI_NC003923 tpi (triosephosphate isomerase) Staphylococcus 21281729 aureus YQI_NC003923 yqi (acetyl-CoA C-acetyltransferase Staphylococcus 21281729 homologue) aureus GALE_AF513299 galE (galactose epimerase) Francisella 23506418 tularensis VVHA_NC004460 vVhA (cytotoxin, cytolysin precursor) Vibrio vulnificus 27366463 TDH_NC004605 tdh (thermostable direct hemolysin A) Vibrio 28899855 parahaemolyticus AGR-II_NC002745 agr-II (accessory gene regulator-II) Staphylococcus 29165615 aureus PARC_NC003997 parC (topoisomerase IV) Bacillus anthracis 30260195 GYRA_AY291534 gyrA (DNA gyrase subunit A) Bacillus anthracis 31323274 AGR-I_AJ617706 agr-I (accessory gene regulator-I) Staphylococcus 46019543 aureus AGR-IV_AJ617711 agr-IV (accessory gene regulator-III) Staphylococcus 46019563 aureus BLAZ_NC002952 blaZ (beta lactamase III) Staphylococcus 49482253 aureus ERMA_NC002952 ermA (rRNA methyltransferase A) Staphylococcus 49482253 aureus ERMB_Y13600 ermB (rRNA methyltransferase B) Staphylococcus 49482253 aureus SEA-SEE_NC002952 sea (staphylococcal enterotoxin A Staphylococcus 49482253 precursor) aureus SEA-SEE_NC002952 sea (staphylococcal enterotoxin A Staphylococcus 49482253 precursor) aureus SEE_NC002952 sea (staphylococcal enterotoxin A Staphylococcus 49482253 precursor) aureus SEH_NC002953 seh (staphylococcal enterotoxin H) Staphylococcus 49484912 aureus ERMC_NC005908 ermC (rRNA methyltransferase C) Staphylococcus 49489772 aureus MUTS_AY698802 mutS (DNA mismatch repair protein) Shigella boydii 52698233 NUC_NC002758 nuc (staphylococcal nuclease) Staphylococcus 57634611 aureus SEB_NC002758 seb (enterotoxin type B precursor) Staphylococcus 57634611 aureus SEG_NC002758 seg (staphylococcal enterotoxin G) Staphylococcus 57634611 aureus SEI_NC002758 sei (staphylococcal enterotoxin I) Staphylococcus 57634611 aureus TSST_NC002758 tsst (toxic shock syndrome toxin-1) Staphylococcus 57634611 aureus TUFB_NC002758 tufB (Elongation factor Tu) Staphylococcus 57634611 aureus Note: artificial reference sequences represent concatenations of partial gene extractions from the indicated reference gi number. Partial sequences were used to create the concatenated sequence because complete gene sequences were not necessary for primer design.

Example 2 Sample Preparation and PCR

Genomic DNA was prepared from samples using the DNeasy Tissue Kit (Qiagen, Valencia, Calif.) according to the manufacturer's protocols.

All PCR reactions were assembled in 50 μL reaction volumes in a 96-well microtiter plate format using a Packard MPII liquid handling robotic platform and M. J. Dyad thermocyclers (MJ research, Waltham, Mass.) or Eppendorf Mastercycler thermocyclers (Eppendorf, Westbury, NY). The PCR reaction mixture consisted of 4 units of Amplitaq Gold, 1× buffer II (Applied Biosystems, Foster City, Calif.), 1.5 mM MgCl₂, 0.4 M betaine, 800 μM dNTP mixture and 250 nM of each primer. The following typical PCR conditions were used: 95° C. for 10 min followed by 8 cycles of 95° C. for 30 seconds, 48° C. for 30 seconds, and 72° C. 30 seconds with the 48° C. annealing temperature increasing 0.9° C. with each of the eight cycles. The PCR was then continued for 37 additional cycles of 95° C for 15 seconds, 56° C. for 20 seconds, and 72° C. 20 seconds.

Example 3 Purification of PCR Products for Mass Spectrometry with Ion Exchange Resin-Magnetic Beads

For solution capture of nucleic acids with ion exchange resin linked to magnetic beads, 25 μl of a 2.5 mg/mL suspension of BioClone amine terminated superparamagnetic beads were added to 25 to 50 μl of a PCR (or RT-PCR) reaction containing approximately 10 μM of a typical PCR amplification product. The above suspension was mixed for approximately 5 minutes by vortexing or pipetting, after which the liquid was removed after using a magnetic separator. The beads containing bound PCR amplification product were then washed three times with 50 mM ammonium bicarbonate/50% MeOH or 100 mM ammonium bicarbonate/50% MeOH, followed by three more washes with 50% MEOH. The bound PCR amplicon was eluted with a solution of 25 mM piperidine, 25 mM imidazole, 35% MeOH which included peptide calibration standards.

Example 4 Mass Spectrometry and Base Composition Analysis

The ESI-FTICR mass spectrometer is based on a Bruker Daltonics (Billerica, MA) Apex II 70e electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer that employs an actively shielded 7 Tesla superconducting magnet. The active shielding constrains the majority of the fringing magnetic field from the superconducting magnet to a relatively small volume. Thus, components that might be adversely affected by stray magnetic fields, such as CRT monitors, robotic components, and other electronics, can operate in close proximity to the FTICR spectrometer. All aspects of pulse sequence control and data acquisition were performed on a 600 MHz Pentium II data station running Bruker's Xmass software under Windows NT 4.0 operating system. Sample aliquots, typically 15 μl, were extracted directly from 96-well microtiter plates using a CTC HTS PAL autosampler (LEAP Technologies, Carrboro, N.C.) triggered by the FTICR data station. Samples were injected directly into a 10 μl sample loop integrated with a fluidics handling system that supplies the 100 μl/hr flow rate to the ESI source. Ions were formed via electrospray ionization in a modified Analytica (Branford, Conn.) source employing an off axis, grounded electrospray probe positioned approximately 1.5 cm from the metalized terminus of a glass desolvation capillary. The atmospheric pressure end of the glass capillary was biased at 6000 V relative to the ESI needle during data acquisition. A counter-current flow of dry N₂ was employed to assist in the desolvation process. Ions were accumulated in an external ion reservoir comprised of an rf-only hexapole, a skimmer cone, and an auxiliary gate electrode, prior to injection into the trapped ion cell where they were mass analyzed. Ionization duty cycles greater than 99% were achieved by simultaneously accumulating ions in the external ion reservoir during ion detection. Each detection event consisted of 1 M data points digitized over 2.3 s. To improve the signal-to-noise ratio (S/N), 32 scans were co-added for a total data acquisition time of 74 s.

The ESI-TOF mass spectrometer is based on a Bruker Daltonics MicroTOF™. Ions from the ESI source undergo orthogonal ion extraction and are focused in a reflectron prior to detection. The TOF and FTICR are equipped with the same automated sample handling and fluidics described above. Ions are formed in the standard MicroTOF™ ESI source that is equipped with the same off-axis sprayer and glass capillary as the FTICR ESI source. Consequently, source conditions were the same as those described above. External ion accumulation was also employed to improve ionization duty cycle during data acquisition. Each detection event on the TOF was comprised of 75,000 data points digitized over 75 μs.

The sample delivery scheme allows sample aliquots to be rapidly injected into the electrospray source at high flow rate and subsequently be electrosprayed at a much lower flow rate for improved ESI sensitivity. Prior to injecting a sample, a bolus of buffer was injected at a high flow rate to rinse the transfer line and spray needle to avoid sample contamination/carryover. Following the rinse step, the autosampler injected the next sample and the flow rate was switched to low flow. Following a brief equilibration delay, data acquisition commenced. As spectra were co-added, the autosampler continued rinsing the syringe and picking up buffer to rinse the injector and sample transfer line. In general, two syringe rinses and one injector rinse were required to minimize sample carryover. During a routine screening protocol a new sample mixture was injected every 106 seconds. More recently a fast wash station for the syringe needle has been implemented which, when combined with shorter acquisition times, facilitates the acquisition of mass spectra at a rate of just under one spectrum/minute.

Raw mass spectra were post-calibrated with an internal mass standard and deconvoluted to monoisotopic molecular masses. Unambiguous base compositions were derived from the exact mass measurements of the complementary single-stranded oligonucleotides. Quantitative results are obtained by comparing the peak heights with an internal PCR calibration standard present in every PCR well at 500 molecules per well. Calibration methods are commonly owned and disclosed in U.S. Provisional Patent Application Ser. No. 60/545,425 which is incorporated herein by reference in entirety.

Example 5 De Novo Determination of Base Composition of Amplification Products using Molecular Mass Modified Deoxynucleotide Triphosphates

Because the molecular masses of the four natural nucleobases have a relatively narrow molecular mass range (A=313.058, G=329.052, C=289.046, T=304.046—See Table 4), a persistent source of ambiguity in assignment of base composition can occur as follows: two nucleic acid strands having different base composition may have a difference of about 1 Da when the base composition difference between the two strands is G⇄A (−15.994) combined with C⇄T (+15.000). For example, one 99-mer nucleic acid strand having a base composition of A₂₇G₃₀C₂₁T₂₁ has a theoretical molecular mass of 30779.058 while another 99-mer nucleic acid strand having a base composition of A₂₆G₃₁C₂₂T₂₀ has a theoretical molecular mass of 30780.052. A 1 Da difference in molecular mass may be within the experimental error of a molecular mass measurement and thus, the relatively narrow molecular mass range of the four natural nucleobases imposes an uncertainty factor.

The present invention provides for a means for removing this theoretical 1 Da uncertainty factor through amplification of a nucleic acid with one mass-tagged nucleobase and three natural nucleobases. The term “nucleobase” as used herein is synonymous with other terms in use in the art including “nucleotide,” “deoxynucleotide,” “nucleotide residue,” “deoxynucleotide residue,” “nucleotide triphosphate (NTP),” or deoxynucleotide triphosphate (dNTP).

Addition of significant mass to one of the 4 nucleobases (dNTPs) in an amplification reaction, or in the primers themselves, will result in a significant difference in mass of the resulting amplification product (significantly greater than 1 Da) arising from ambiguities arising from the G A combined with C⇄T event (Table 4). Thus, the same the G⇄A (−15.994) event combined with 5-Iodo-C⇄T (−110.900) event would result in a molecular mass difference of 126.894. If the molecular mass of the base composition A₂₇G₃₀ 5-Iodo-C₂₁T₂₁ (33422.958) is compared with A₂₆G₃₁5-Iodo-C₂₂T₂₀, (33549.852) the theoretical molecular mass difference is +126.894. The experimental error of a molecular mass measurement is not significant with regard to this molecular mass difference. Furthermore, the only base composition consistent with a measured molecular mass of the 99-mer nucleic acid is A₂₇G₃₀5-Iodo-C₂₁T₂₁. In contrast, the analogous amplification without the mass tag has 18 possible base compositions. TABLE 4 Molecular Masses of Natural Nucleobases and the Mass-Modified Nucleobase 5-Iodo-C and Molecular Mass Differences Resulting from Transitions Nucleobase Molecular Mass Transition Molecular Mass A 313.058 A-->T −9.012 A 313.058 A-->C −24.012 A 313.058 A-->5-Iodo-C 101.888 A 313.058 A-->G 15.994 T 304.046 T-->A 9.012 T 304.046 T-->C −15.000 T 304.046 T-->5-Iodo-C 110.900 T 304.046 T-->G 25.006 C 289.046 C-->A 24.012 C 289.046 C-->T 15.000 C 289.046 C-->G 40.006 5-Iodo-C 414.946 5-Iodo-C-->A −101.888 5-Iodo-C 414.946 5-Iodo-C-->T −110.900 5-Iodo-C 414.946 5-Iodo-C-->G −85.894 G 329.052 G-->A −15.994 G 329.052 G-->T −25.006 G 329.052 G-->C −40.006 G 329.052 G-->5-Iodo-C 85.894

Mass spectra of bioagent-identifying amplicons were analyzed independently using a maximum-likelihood processor, such as is widely used in radar signal processing. This processor, referred to as GenX, first makes maximum likelihood estimates of the input to the mass spectrometer for each primer by running matched filters for each base composition aggregate on the input data. This includes the GenX response to a calibrant for each primer.

The algoritlun emphasizes performance predictions culminating in probability-of-detection versus probability-of-false-alarm plots for conditions involving complex backgrounds of naturally occurring organisms and environmental contaminants. Matched filters consist of a priori expectations of signal values given the set of primers used for each of the bioagents. A genomic sequence database is used to define the mass base count matched filters. The database contains the sequences of known bacterial bioagents and includes threat organisms as well as benign background organisms. The latter is used to estimate and subtract the spectral signature produced by the background organisms. A maximum likelihood detection of known background organisms is implemented using matched filters and a running-sum estimate of the noise covariance. Background signal strengths are estimated and used along with the matched filters to form signatures which are then subtracted. The maximum likelihood process is applied to this “cleaned up” data in a similar manner employing matched filters for the organisms and a running-sum estimate of the noise-covariance for the cleaned up data.

The amplitudes of all base compositions of bioagent-identifying amplicons for each primer are calibrated and a final maximum likelihood amplitude estimate per organism is made based upon the multiple single primer estimates. Models of all system noise are factored into this two-stage maximum likelihood calculation. The processor reports the number of molecules of each base composition contained in the spectra. The quantity of amplification product corresponding to the appropriate primer set is reported as well as the quantities of primers remaining upon completion of the amplification reaction.

Base count blurring can be carried out as follows. “Electronic PCR” can be conducted on nucleotide sequences of the desired bioagents to obtain the different expected base counts that could be obtained for each primer pair. See for example, ncbi.nlm.nih.gov/sutils/e-pcr/; Schuler, Genome Res. 7:541-50, 1997. In one illustrative embodiment, one or more spreadsheets, such as Microsoft Excel workbooks contain a plurality of worksheets. First in this example, there is a worksheet with a name similar to the workbook name; this worksheet contains the raw electronic PCR data. Second, there is a worksheet named “filtered bioagents base count” that contains bioagent name and base count; there is a separate record for each strain after removing sequences that are not identified with a genus and species and removing all sequences for bioagents with less than 10 strains. Third, there is a worksheet, “Sheet1” that contains the frequency of substitutions, insertions, or deletions for this primer pair. This data is generated by first creating a pivot table from the data in the “filtered bioagents base count” worksheet and then executing an Excel VBA macro. The macro creates a table of differences in base counts for bioagents of the same species, but different strains. One of ordinary skill in the art may understand additional pathways for obtaining similar table differences without undo experimentation.

Application of an exemplary script, involves the user defining a threshold that specifies the fraction of the strains that are represented by the reference set of base counts for each bioagent. The reference set of base counts for each bioagent may contain as many different base counts as are needed to meet or exceed the threshold. The set of reference base counts is defined by taking the most abundant strain's base type composition and adding it to the reference set and then the next most abundant strain's base type composition is added until the threshold is met or exceeded. The current set of data was obtained using a threshold of 55%, which was obtained empirically.

For each base count not included in the reference base count set for that bioagent, the script then proceeds to determine the manner in which the current base count differs from each of the base counts in the reference set. This difference may be represented as a combination of substitutions, Si=Xi, and insertions, Ii=Yi, or deletions, Di=Zi. If there is more than one reference base count, then the reported difference is chosen using rules that aim to minimize the number of changes and, in instances with the same number of changes, minimize the number of insertions or deletions. Therefore, the primary rule is to identify the difference with the minimum sum (Xi+Yi) or (Xi+Zi), e.g., one insertion rather than two substitutions. If there are two or more differences with the minimum sum, then the one that will be reported is the one that contains the most substitutions.

Differences between a base count and a reference composition are categorized as one, two, or more substitutions, one, two, or more insertions, one, two, or more deletions, and combinations of substitutions and insertions or deletions. The different classes of nucleobase changes and their probabilities of occurrence have been delineated in U.S. Patent Application Publication No. 2004209260 (U.S. application Ser. No. 10/418,514) which is incorporated herein by reference in entirety.

Example 6 Use of Broad Range Survey and Division Wide Primer Pairs for Identification of Bacteria in an Epidemic Surveillance Investigation

This investigation employed a set of 16 primer pairs which is herein designated the “surveillance primer set” and comprises broad range survey primer pairs, division wide primer pairs and a single Bacillus lade primer pair. The surveillance primer set is shown in Table 5 and consists of primer pairs originally listed in Table 2. This surveillance set comprises primers with T modifications (note TMOD designation in primer names) which constitutes a functional improvement with regard to prevention of non-templated adenylation (vide supra) relative to originally selected primers which are displayed below in the same row. Primer pair 449 (non-T modified) has been modified twice. Its predecessors are primer pairs 70 and 357, displayed below in the same row. Primer pair 360 has also been modified twice and its predecessors are primer pairs 17 and 118. TABLE 5 Bacterial Primer Pairs of the Surveillance Primer Set Forward Reverse Primer Primer Primer Pair (SEQ ID (SEQ ID No. Forward Primer Name NO:) Reverse Primer Name NO:) Target Gene 346 16S_EC_713_732_TMOD_F 202 16S_EC_789_809_TMOD_R 1110 16S rRNA 10 16S_EC_713_732_F 21 16S_EC_789_809 798 16S rRNA 347 16S_EC_785_806_TMOD_F 560 16S_EC_880_897_TMOD_R 1278 16S rRNA 11 16S_EC_785_806_F 118 16S_EC_880_897_R 830 16S rRNA 348 16S_EC_960_981_TMOD_F 706 16S_EC_1054_1073_TMOD_R 895 16S rRNA 14 16S_EC_960_981_F 672 16S_EC_1054_1073_R 735 16S rRNA 349 23S_EC_1826_1843_TMOD_F 401 23S_EC_1906_1924_TMOD_R 1156 23S rRNA 16 23S_EC_1826_1843_F 80 23S_EC_1906_1924_R 805 23S rRNA 352 INFB_EC_1365_1393_TMOD_F 687 INFB_EC_1439_1467_TMOD_R 1411 infB 34 INFB_EC_1365_1393_F 524 INFB_EC_1439_1467_R 1248 infB 354 RPOC_EC_2218_2241_TMOD_F 405 RPOC_EC_2313_2337_TMOD_R 1072 rpoC 52 RPOC_EC_2218_2241_F 81 RPOC_EC_2313_2337_R 790 rpoC 355 SSPE_BA_115_137_TMOD_F 255 SSPE_BA_197_222_TMOD_R 1402 sspE 58 SSPE_BA_115_137_F 45 SSPE_BA_197_222_R 1201 sspE 356 RPLB_EC_650_679_TMOD_F 232 RPLB_EC_739_762_TMOD_R 592 rplB 66 RPLB_EC_650_679_F 98 RPLB_EC_739_762_R 999 rplB 358 VALS_EC_1105_1124_TMOD_F 385 VALS_EC_1195_1218_TMOD_R 1093 valS 71 VALS_EC_1105_1124_F 77 VALS_EC_1195_1218_R 795 valS 359 RPOB_EC_1845_1866_TMOD_F 659 RPOB_EC_1909_1929_TMOD_R 1250 rpoB 72 RPOB_EC_1845_1866_F 233 RPOB_EC_1909_1929_R 825 rpoB 360 23S_EC_2646_2667_TMOD_F 409 23S_EC_2745_2765_TMOD_R 1434 23S rRNA 118 23S_EC_2646_2667_F 84 23S_EC_2745_2765_R 1389 23S rRNA 17 23S_EC_2645_2669_F 408 23S_EC_2744_2761_R 1252 23S rRNA 361 16S_EC_1090_1111_2_TMOD_F 697 16S_EC_1175_1196_TMOD_R 1398 16S rRNA 3 16S_EC_1090_1111_2_F 651 16S_EC_1175_1196_R 1159 16S rRNA 362 RPOB_EC_3799_3821_TMOD_F 581 RPOB_EC_3862_3888_TMOD_R 1325 rpoB 289 RPOB_EC_3799_3821_F 124 RPOB_EC_3862_3888_R 840 rpoB 363 RPOC_EC_2146_2174_TMOD_F 284 RPOC_EC_2227_2245_TMOD_R 898 rpoC 290 RPOC_EC_2146_2174_F 52 RPOC_EC_2227_2245_R 736 rpoC 367 TUFB_EC_957_979_TMOD_F 308 TUFB_EC_1034_1058_TMOD_R 1276 tufB 293 TUFB_EC_957_979_F 55 TUFB_EC_1034_1058_R 829 tufB 449 RPLB_EC_690_710_F 309 RPLB_EC_737_758_R 1336 rplB 357 RPLB_EC_688_710_TMOD_F 296 RPLB_EC_736_757_TMOD_R 1337 rplB 67 RPLB_EC_688_710_F 54 RPLB_EC_736_757_R 842 rplB

The 16 primer pairs of the surveillance set are used to produce bioagent identifying amplicons whose base compositions are sufficiently different amongst all known bacteria at the species level to identify, at a reasonable confidence level, any given bacterium at the species level. As shown in Tables 6A-E, common respiratory bacterial pathogens can be distinguished by the base compositions of bioagent identifying amplicons obtained using the 16 primer pairs of the surveillance set. In some cases, triangulation identification improves the confidence level for species assignment. For example, nucleic acid from Strepococcus pyogenes can be amplified by nine of the sixteen surveillance primer pairs and Streptococcus pneumoniae can be amplified by ten of the sixteen surveillance primer pairs. The base compositions of the bioagent identifying amplicons are identical for only one of the analogous bioagent identifying amplicons and differ in all of the remaining analogous bioagent identifying amplicons by up to four bases per bioagent identifying amplicon. The resolving power of the surveillance set was confirmed by determination of base compositions for 120 isolates of respiratory pathogens representing 70 different bacterial species and the results indicated that natural variations (usually only one or two base substitutions per bioagent identifying amplicon) amongst multiple isolates of the same species did not prevent correct identification of major pathogenic organisms at the species level.

Bacillus anthracis is a well known biological warfare agent which has emerged in domestic terrorism in recent years. Since it was envisioned to produce bioagent identifying amplicons for identification of Bacillus anthracis, additional drill-down analysis primers were designed to target genes present on virulence plasmids of Bacillus anthracis so that additional confidence could be reached in positive identification of this pathogenic organism. Three drill-down analysis primers were designed and are listed in Tables 2 and 6. In Table 6, the drill-down set comprises primers with T modifications (note TMOD designation in primer names) which constitutes a functional improvement with regard to prevention of non-templated adenylation (vide supra) relative to originally selected primers which are displayed below in the same row. TABLE 6 Drill-Down Primer Pairs for Confirmation of Identification of Bacillus anthracis Forward Reverse Primer Primer Primer Pair (SEQ ID (SEQ ID No. Forward Primer Name NO:) Reverse Primer Name NO:) Target Gene 350 CAPC_BA_274_303_TMOD_F 476 CAPC_BA_349_376_TMOD_R 1314 capC 24 CAPC_BA_274_303_F 109 CAPC_BA_349_376_R 837 capC 351 CYA_BA_1353_1379_TMOD_F 355 CYA_BA_1448_1467_TMOD_R 1423 cyA 30 CYA_BA_1353_1379_F 64 CYA_BA_1448_1467_R 1342 cyA 353 LEF_BA_756_781_TMOD_F 220 LEF_BA_843_872_TMOD_R 1394 lef 37 LEF_BA_756_781_F 26 LEF_BA_843_872_R 1135 lef

Phylogenetic coverage of bacterial space of the sixteen surveillance primers of Table 5 and the three Bacillus anthracis drill-down primers of Table 6 is shown in FIG. 3 which lists common pathogenic bacteria. FIG. 3 is not meant to be comprehensive in illustrating all species identified by the primers. Only pathogenic bacteria are listed as representative examples of the bacterial species that can be identified by the primers and methods of the present invention. Nucleic acid of groups of bacteria enclosed within the polygons of FIG. 3 can be amplified to obtain bioagent identifying amplicons using the primer pair numbers listed in the upper right hand corner of each polygon. Primer coverage for polygons within polygons is additive. As an illustrative example, bioagent identifying amplicons can be obtained for Chlamydia trachomatis by amplification with, for example, primer pairs 346-349, 360 and 361, but not with any of the remaining primers of the surveillance primer set. On the other hand, bioagent identifying amplicons can be obtained from nucleic acid originating from Bacillus anthracis (located within 5 successive polygons) using, for example, any of the following primer pairs: 346-349, 360, 361 (base polygon), 356, 449 (second polygon), 352 (third polygon), 355 (fourth polygon), 350, 351 and 353 (fifth polygon). Multiple coverage of a given organism with multiple primers provides for increased confidence level in identification of the organism as a result of enabling broad triangulation identification.

In Tables 7A-E, base compositions of respiratory pathogens for primer target regions are shown. Two entries in a cell, represent variation in ribosomal DNA operons. The most predominant base composition is shown first and the minor (frequently a single operon) is indicated by an asterisk (*). Entries with NO DATA mean that the primer would not be expected to prime this species due to mismatches between the primer and target region, as determined by theoretical PCR. TABLE 7A Base Compositions of Common Respiratory Pathogens for Bioagent Identifying Amplicons Corresponding to Primer Pair Nos: 346, 347 and 348 Primer 346 Primer 347 Primer 348 Organism Strain [A G C T] [A G C T] [A G C T] Klebsiella MGH78578 [29 32 25 13] [23 38 28 26] [26 32 28 30] pneumoniae [29 31 25 13]* [23 37 28 26]* [26 31 28 30]* Yersinia pestis CO-92 Biovar [29 32 25 13] [22 39 28 26] [29 30 28 29] Orientalis [30 30 27 29]* Yersinia pestis KIM5 P12 (Biovar [29 32 25 13] [22 39 28 26] [29 30 28 29] Mediaevalis) Yersinia pestis 91001 [29 32 25 13] [22 39 28 26] [29 30 28 29] [30 30 27 29]* Haemophilus KW20 [28 31 23 17] [24 37 25 27] [29 30 28 29] influenzae Pseudomonas PAO1 [30 31 23 15] [26 36 29 24] [26 32 29 29] aeruginosa [27 36 29 23]* Pseudomonas Pf0-1 [30 31 23 15] [26 35 29 25] [28 31 28 29] fluorescens Pseudomonas KT2440 [30 31 23 15] [28 33 27 27] [27 32 29 28] putida Legionella Philadelphia-1 [30 30 24 15] [33 33 23 27] [29 28 28 31] pneumophila Francisella schu 4 [32 29 22 16] [28 38 26 26] [25 32 28 31] tularensis Bordetella Tohama I [30 29 24 16] [23 37 30 24] [30 32 30 26] pertussis Burkholderia J2315 [29 29 27 14] [27 32 26 29] [27 36 31 24] cepacia [20 42 35 19]* Burkholderia K96243 [29 29 27 14] [27 32 26 29] [27 36 31 24] pseudomallei Neisseria FA 1090, ATCC [29 28 24 18] [27 34 26 28] [24 36 29 27] gonorrhoeae 700825 Neisseria MC58 (serogroup B) [29 28 26 16] [27 34 27 27] [25 35 30 26] meningitidis Neisseria serogroup C, FAM18 [29 28 26 16] [27 34 27 27] [25 35 30 26] meningitidis Neisseria Z2491 (serogroup A) [29 28 26 16] [27 34 27 27] [25 35 30 26] meningitidis Chlamydophila TW-183 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Chlamydophila AR39 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Chlamydophila CWL029 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Chlamydophila J138 [31 27 22 19] NO DATA [32 27 27 29] pneumoniae Corynebacterium NCTC13129 [29 34 21 15] [22 38 31 25] [22 33 25 34] diphtheriae Mycobacterium k10 [27 36 21 15] [22 37 30 28] [21 36 27 30] avium Mycobacterium 104 [27 36 21 15] [22 37 30 28] [21 36 27 30] avium Mycobacterium CSU#93 [27 36 21 15] [22 37 30 28] [21 36 27 30] tuberculosis Mycobacterium CDC 1551 [27 36 21 15] [22 37 30 28] [21 36 27 30] tuberculosis Mycobacterium H37Rv (lab strain) [27 36 21 15] [22 37 30 28] [21 36 27 30] tuberculosis Mycoplasma M129 [31 29 19 20] NO DATA NO DATA pneumoniae Staphylococcus MRSA252 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [29 31 30 29]* Staphylococcus MSSA476 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [30 29 29 30]* Staphylococcus COL [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [30 29 29 30]* Staphylococcus Mu50 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [30 29 29 30]* Staphylococcus MW2 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [30 29 29 30]* Staphylococcus N315 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [30 29 29 30]* Staphylococcus NCTC 8325 [27 30 21 21] [25 35 30 26] [30 29 30 29] aureus [25 35 31 26]* [30 29 29 30] Streptococcus NEM316 [26 32 23 18] [24 36 31 25] [25 32 29 30] agalactiae [24 36 30 26]* Streptococcus NC_002955 [26 32 23 18] [23 37 31 25] [29 30 25 32] equi Streptococcus MGAS8232 [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus MGAS315 [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus SSI-1 [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus MGAS10394 [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus Manfredo (M5) [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus SF370 (M1) [26 32 23 18] [24 37 30 25] [25 31 29 31] pyogenes Streptococcus 670 [26 32 23 18] [25 35 28 28] [25 32 29 30] pneumoniae Streptococcus R6 [26 32 23 18] [25 35 28 28] [25 32 29 30] pneumoniae Streptococcus TIGR4 [26 32 23 18] [25 35 28 28] [25 32 30 29] pneumoniae Streptococcus NCTC7868 [25 33 23 18] [24 36 31 25] [25 31 29 31] gordonii Streptococcus NCTC 12261 [26 32 23 18] [25 35 30 26] [25 32 29 30] mitis [24 31 35 29]* Streptococcus UA159 [24 32 24 19] [25 37 30 24] [28 31 26 31] mutans

TABLE 7B Base Compositions of Common Respiratory Pathogens for Bioagent Identifying Amplicons Corresponding to Primer Pair Nos: 349, 360, and 356 Primer 349 Primer 360 Primer 356 Organism Strain [A G C T] [A G C T] [A G C T] Klebsiella MGH78578 [25 31 25 22] [33 37 25 27] NO DATA pneumoniae Yersinia pestis CO-92 Biovar [25 31 27 20] [34 35 25 28] NO DATA Orientalis [25 32 26 20]* Yersinia pestis KIM5 P12 (Biovar [25 31 27 20] [34 35 25 28] NO DATA Mediaevalis) [25 32 26 20]* Yersinia pestis 91001 [25 31 27 20] [34 35 25 28] NO DATA Haemophilus KW20 [28 28 25 20] [32 38 25 27] NO DATA influenzae Pseudomonas PAO1 [24 31 26 20] [31 36 27 27] NO DATA aeruginosa [31 36 27 28]* Pseudomonas Pf0-1 NO DATA [30 37 27 28] NO DATA fluorescens [30 37 27 28] Pseudomonas KT2440 [24 31 26 20] [30 37 27 28] NO DATA putida Legionella Philadelphia-1 [23 30 25 23] [30 39 29 24] NO DATA pneumophila Francisella schu 4 [26 31 25 19] [32 36 27 27] NO DATA tularensis Bordetella Tohama I [21 29 24 18] [33 36 26 27] NO DATA pertussis Burkholderia J2315 [23 27 22 20] [31 37 28 26] NO DATA cepacia Burkholderia K96243 [23 27 22 20] [31 37 28 26] NO DATA pseudomallei Neisseria FA 1090, ATCC 700825 [24 27 24 17] [34 37 25 26] NO DATA gonorrhoeae Neisseria MC58 (serogroup B) [25 27 22 18] [34 37 25 26] NO DATA meningitidis Neisseria serogroup C, FAM18 [25 26 23 18] [34 37 25 26] NO DATA meningitidis Neisseria Z2491 (serogroup A) [25 26 23 18] [34 37 25 26] NO DATA meningitidis Chlamydophila TW-183 [30 28 27 18] NO DATA NO DATA pneumoniae Chlamydophila AR39 [30 28 27 18] NO DATA NO DATA pneumoniae Chlamydophila CWL029 [30 28 27 18] NO DATA NO DATA pneumoniae Chlamydophila J138 [30 28 27 18] NO DATA NO DATA pneumoniae Corynebacterium NCTC13129 NO DATA [29 40 28 25] NO DATA diphtheriae Mycobacterium k10 NO DATA [33 35 32 22] NO DATA avium Mycobacterium 104 NO DATA [33 35 32 22] NO DATA avium Mycobacterium CSU#93 NO DATA [30 36 34 22] NO DATA tuberculosis Mycobacterium CDC 1551 NO DATA [30 36 34 22] NO DATA tuberculosis Mycobacterium H37Rv (lab strain) NO DATA [30 36 34 22] NO DATA tuberculosis Mycoplasma M129 [28 30 24 19] [34 31 29 28] NO DATA pneumoniae Staphylococcus MRSA252 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Staphylococcus MSSA476 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Staphylococcus COL [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Staphylococcus Mu50 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Staphylococcus MW2 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Staphylococcus N315 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Staphylococcus NCTC 8325 [26 30 25 20] [31 38 24 29] [33 30 31 27] aureus Streptococcus NEM316 [28 31 22 20] [33 37 24 28] [37 30 28 26] agalactiae Streptococcus NC_002955 [28 31 23 19] [33 38 24 27] [37 31 28 25] equi Streptococcus MGAS8232 [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus MGAS315 [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus SSI-1 [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus MGAS10394 [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus Manfredo (M5) [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes Streptococcus SF370 (M1) [28 31 23 19] [33 37 24 28] [38 31 29 23] pyogenes [28 31 22 20]* Streptococcus 670 [28 31 22 20] [34 36 24 28] [37 30 29 25] pneumoniae Streptococcus R6 [28 31 22 20] [34 36 24 28] [37 30 29 25] pneumoniae Streptococcus TIGR4 [28 31 22 20] [34 36 24 28] [37 30 29 25] pneumoniae Streptococcus NCTC7868 [28 32 23 20] [34 36 24 28] [36 31 29 25] gordonii Streptococcus NCTC 12261 [28 31 22 20] [34 36 24 28] [37 30 29 25] mitis [29 30 22 20]* Streptococcus UA159 [26 32 23 22] [34 37 24 27] NO DATA mutans

TABLE 7C Base Compositions of Common Respiratory Pathogens for Bioagent Identifying Amplicons Corresponding to Primer Pair Nos: 449, 354, and 352 Primer 449 Primer 354 Primer 352 Organism Strain [A G C T] [A G C T] [A G C T] Klebsiella MGH78578 NO DATA [27 33 36 26] NO DATA pneumoniae Yersinia pestis CO-92 Biovar NO DATA [29 31 33 29] [32 28 20 25] Orientalis Yersinia pestis KIM5 P12 (Biovar NO DATA [29 31 33 29] [32 28 20 25] Mediaevalis) Yersinia pestis 91001 NO DATA [29 31 33 29] NO DATA Haemophilus KW20 NO DATA [30 29 31 32] NO DATA influenzae Pseudomonas PAO1 NO DATA [26 33 39 24] NO DATA aeruginosa Pseudomonas Pf0-1 NO DATA [26 33 34 29] NO DATA fluorescens Pseudomonas KT2440 NO DATA [25 34 36 27] NO DATA putida Legionella Philadelphia-1 NO DATA NO DATA NO DATA pneumophila Francisella schu 4 NO DATA [33 32 25 32] NO DATA tularensis Bordetella Tohama I NO DATA [26 33 39 24] NO DATA pertussis Burkholderia J2315 NO DATA [25 37 33 27] NO DATA cepacia Burkholderia K96243 NO DATA [25 37 34 26] NO DATA pseudomallei Neisseria FA 1090, ATCC 700825 [17 23 22 10] [29 31 32 30] NO DATA gonorrhoeae Neisseria MC58 (serogroup B) NO DATA [29 30 32 31] NO DATA meningitidis Neisseria serogroup C, FAM18 NO DATA [29 30 32 31] NO DATA meningitidis Neisseria Z2491 (serogroup A) NO DATA [29 30 32 31] NO DATA meningitidis Chlamydophila TW-183 NO DATA NO DATA NO DATA pneumoniae Chlamydophila AR39 NO DATA NO DATA NO DATA pneumoniae Chlamydophila CWL029 NO DATA NO DATA NO DATA pneumoniae Chlamydophila J138 NO DATA NO DATA NO DATA pneumoniae Corynebacterium NCTC13129 NO DATA NO DATA NO DATA diphtheriae Mycobacterium k10 NO DATA NO DATA NO DATA avium Mycobacterium 104 NO DATA NO DATA NO DATA avium Mycobacterium CSU#93 NO DATA NO DATA NO DATA tuberculosis Mycobacterium CDC 1551 NO DATA NO DATA NO DATA tuberculosis Mycobacterium H37Rv (lab strain) NO DATA NO DATA NO DATA tuberculosis Mycoplasma M129 NO DATA NO DATA NO DATA pneumoniae Staphylococcus MRSA252 [17 20 21 17] [30 27 30 35] [36 24 19 26] aureus Staphylococcus MSSA476 [17 20 21 17] [30 27 30 35] [36 24 19 26] aureus Staphylococcus COL [17 20 21 17] [30 27 30 35] [35 24 19 27] aureus Staphylococcus Mu50 [17 20 21 17] [30 27 30 35] [36 24 19 26] aureus Staphylococcus MW2 [17 20 21 17] [30 27 30 35] [36 24 19 26] aureus Staphylococcus N315 [17 20 21 17] [30 27 30 35] [36 24 19 26] aureus Staphylococcus NCTC 8325 [17 20 21 17] [30 27 30 35] [35 24 19 27] aureus Streptococcus NEM316 [22 20 19 14] [26 31 27 38] [29 26 22 28] agalactiae Streptococcus NC_002955 [22 21 19 13] NO DATA NO DATA equi Streptococcus MGAS8232 [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus MGAS315 [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus SSI-1 [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus MGAS10394 [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus Manfredo (M5) [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus SF370 (M1) [23 21 19 12] [24 32 30 36] NO DATA pyogenes Streptococcus 670 [22 20 19 14] [25 33 29 35] [30 29 21 25] pneumoniae Streptococcus R6 [22 20 19 14] [25 33 29 35] [30 29 21 25] pneumoniae Streptococcus TIGR4 [22 20 19 14] [25 33 29 35] [30 29 21 25] pneumoniae Streptococcus NCTC7868 [21 21 19 14] NO DATA [29 26 22 28] gordonii Streptococcus NCTC 12261 [22 20 19 14] [26 30 32 34] NO DATA mitis Streptococcus UA159 NO DATA NO DATA NO DATA mutans

TABLE 7D Base Compositions of Common Respiratory Pathogens for Bioagent Identifying Amplicons Corresponding to Primer Pair Nos: 355, 358, and 359 Primer 355 Primer 358 Primer 359 Organism Strain [A G C T] [A G C T] [A G C T] Klebsiella MGH78578 NO DATA [24 39 33 20] [25 21 24 17] pneumoniae Yersinia pestis CO-92 Biovar NO DATA [26 34 35 21] [23 23 19 22] Orientalis Yersinia pestis KIM5 P12 (Biovar NO DATA [26 34 35 21] [23 23 19 22] Mediaevalis) Yersinia pestis 91001 NO DATA [26 34 35 21] [23 23 19 22] Haemophilus KW20 NO DATA NO DATA NO DATA influenzae Pseudomonas PAO1 NO DATA NO DATA NO DATA aeruginosa Pseudomonas Pf0-1 NO DATA NO DATA NO DATA fluorescens Pseudomonas KT2440 NO DATA [21 37 37 21] NO DATA putida Legionella Philadelphia-1 NO DATA NO DATA NO DATA pneumophila Francisella schu 4 NO DATA NO DATA NO DATA tularensis Bordetella Tohama I NO DATA NO DATA NO DATA pertussis Burkholderia J2315 NO DATA NO DATA NO DATA cepacia Burkholderia K96243 NO DATA NO DATA NO DATA pseudomallei Neisseria FA 1090, ATCC 700825 NO DATA NO DATA NO DATA gonorrhoeae Neisseria MC58 (serogroup B) NO DATA NO DATA NO DATA meningitidis Neisseria serogroup C, FAM18 NO DATA NO DATA NO DATA meningitidis Neisseria Z2491 (serogroup A) NO DATA NO DATA NO DATA meningitidis Chlamydophila TW-183 NO DATA NO DATA NO DATA pneumoniae Chlamydophila AR39 NO DATA NO DATA NO DATA pneumoniae Chlamydophila CWL029 NO DATA NO DATA NO DATA pneumoniae Chlamydophila J138 NO DATA NO DATA NO DATA pneumoniae Corynebacterium NCTC13129 NO DATA NO DATA NO DATA diphtheriae Mycobacterium k10 NO DATA NO DATA NO DATA avium Mycobacterium 104 NO DATA NO DATA NO DATA avium Mycobacterium CSU#93 NO DATA NO DATA NO DATA tuberculosis Mycobacterium CDC 1551 NO DATA NO DATA NO DATA tuberculosis Mycobacterium H37Rv (lab strain) NO DATA NO DATA NO DATA tuberculosis Mycoplasma M129 NO DATA NO DATA NO DATA pneumoniae Staphylococcus MRSA252 NO DATA NO DATA NO DATA aureus Staphylococcus MSSA476 NO DATA NO DATA NO DATA aureus Staphylococcus COL NO DATA NO DATA NO DATA aureus Staphylococcus Mu50 NO DATA NO DATA NO DATA aureus Staphylococcus MW2 NO DATA NO DATA NO DATA aureus Staphylococcus N315 NO DATA NO DATA NO DATA aureus Staphylococcus NCTC 8325 NO DATA NO DATA NO DATA aureus Streptococcus NEM316 NO DATA NO DATA NO DATA agalactiae Streptococcus NC_002955 NO DATA NO DATA NO DATA equi Streptococcus MGAS8232 NO DATA NO DATA NO DATA pyogenes Streptococcus MGAS315 NO DATA NO DATA NO DATA pyogenes Streptococcus SSI-1 NO DATA NO DATA NO DATA pyogenes Streptococcus MGAS10394 NO DATA NO DATA NO DATA pyogenes Streptococcus Manfredo (M5) NO DATA NO DATA NO DATA pyogenes Streptococcus SF370 (M1) NO DATA NO DATA NO DATA pyogenes Streptococcus 670 NO DATA NO DATA NO DATA pneumoniae Streptococcus R6 NO DATA NO DATA NO DATA pneumoniae Streptococcus TIGR4 NO DATA NO DATA NO DATA pneumoniae Streptococcus NCTC7868 NO DATA NO DATA NO DATA gordonii Streptococcus NCTC 12261 NO DATA NO DATA NO DATA mitis Streptococcus UA159 NO DATA NO DATA NO DATA mutans

TABLE 7E Base Compositions of Common Respiratory Pathogens for Bioagent Identifying Amplicons Corresponding to Primer Pair Nos: 362, 363, and 367 Primer 362 Primer 363 Primer 367 Organism Strain [A G C T] [A G C T] [A G C T] Klebsiella MGH78578 [21 33 22 16] [16 34 26 26] NO DATA pneumoniae Yersinia pestis CO-92 Biovar [20 34 18 20] NO DATA NO DATA Orientalis Yersinia pestis KIM5 P12 (Biovar [20 34 18 20] NO DATA NO DATA Mediaevalis) Yersinia pestis 91001 [20 34 18 20] NO DATA NO DATA Haemophilus KW20 NO DATA NO DATA NO DATA influenzae Pseudomonas PAO1 [19 35 21 17] [16 36 28 22] NO DATA aeruginosa Pseudomonas Pf0-1 NO DATA [18 35 26 23] NO DATA fluorescens Pseudomonas KT2440 NO DATA [16 35 28 23] NO DATA putida Legionella Philadelphia-1 NO DATA NO DATA NO DATA pneumophila Francisella schu 4 NO DATA NO DATA NO DATA tularensis Bordetella Tohama I [20 31 24 17] [15 34 32 21] [26 25 34 19] pertussis Burkholderia J2315 [20 33 21 18] [15 36 26 25] [25 27 32 20] cepacia Burkholderia K96243 [19 34 19 20] [15 37 28 22] [25 27 32 20] pseudomallei Neisseria FA 1090, ATCC 700825 NO DATA NO DATA NO DATA gonorrhoeae Neisseria MC58 (serogroup B) NO DATA NO DATA NO DATA meningitidis Neisseria serogroup C, FAM18 NO DATA NO DATA NO DATA meningitidis Neisseria Z2491 (serogroup A) NO DATA NO DATA NO DATA meningitidis Chlamydophila TW-183 NO DATA NO DATA NO DATA pneumoniae Chlamydophila AR39 NO DATA NO DATA NO DATA pneumoniae Chlamydophila CWL029 NO DATA NO DATA NO DATA pneumoniae Chlamydophila J138 NO DATA NO DATA NO DATA pneumoniae Corynebacterium NCTC13129 NO DATA NO DATA NO DATA diphtheriae Mycobacterium k10 [19 34 23 16] NO DATA [24 26 35 19] avium Mycobacterium 104 [19 34 23 16] NO DATA [24 26 35 19] avium Mycobacterium CSU#93 [19 31 25 17] NO DATA [25 25 34 20] tuberculosis Mycobacterium CDC 1551 [19 31 24 18] NO DATA [25 25 34 20] tuberculosis Mycobacterium H37Rv (lab strain) [19 31 24 18] NO DATA [25 25 34 20] tuberculosis Mycoplasma M129 NO DATA NO DATA NO DATA pneumoniae Staphylococcus MRSA252 NO DATA NO DATA NO DATA aureus Staphylococcus MSSA476 NO DATA NO DATA NO DATA aureus Staphylococcus COL NO DATA NO DATA NO DATA aureus Staphylococcus Mu50 NO DATA NO DATA NO DATA aureus Staphylococcus MW2 NO DATA NO DATA NO DATA aureus Staphylococcus N315 NO DATA NO DATA NO DATA aureus Staphylococcus NCTC 8325 NO DATA NO DATA NO DATA aureus Streptococcus NEM316 NO DATA NO DATA NO DATA agalactiae Streptococcus NC_002955 NO DATA NO DATA NO DATA equi Streptococcus MGAS8232 NO DATA NO DATA NO DATA pyogenes Streptococcus MGAS315 NO DATA NO DATA NO DATA pyogenes Streptococcus SSI-1 NO DATA NO DATA NO DATA pyogenes Streptococcus MGAS10394 NO DATA NO DATA NO DATA pyogenes Streptococcus Manfredo (M5) NO DATA NO DATA NO DATA pyogenes Streptococcus SF370 (M1) NO DATA NO DATA NO DATA pyogenes Streptococcus 670 NO DATA NO DATA NO DATA pneumoniae Streptococcus R6 [20 30 19 23] NO DATA NO DATA pneumoniae Streptococcus TIGR4 [20 30 19 23] NO DATA NO DATA pneumoniae Streptococcus NCTC7868 NO DATA NO DATA NO DATA gordonii Streptococcus NCTC 12261 NO DATA NO DATA NO DATA mitis Streptococcus UA159 NO DATA NO DATA NO DATA mutans

Four sets of throat samples from military recruits at different military facilities taken at different time points were analyzed using the primers of the present invention. The first set was collected at a military training center from Nov. 1 to Dec. 20, 2002 during one of the most severe outbreaks of pneumonia associated with group A Streptococcus in the United States since 1968. During this outbreak, fifty-one throat swabs were taken from both healthy and hospitalized recruits and plated on blood agar for selection of putative group A Streptococcus colonies. A second set of 15 original patient specimens was taken during the height of this group A Streptococcus-associated respiratory disease outbreak. The third set were historical samples, including twenty-seven isolates of group A Streptococcus, from disease outbreaks at this and other military training facilities during previous years. The fourth set of samples was collected from five geographically separated military facilities in the continental U.S. in the winter immediately following the severe November/December 2002 outbreak.

Pure colonies isolated from group A Streptococcus-selective media from all four collection periods were analyzed with the surveillance primer set. All samples showed base compositions that precisely matched the four completely sequenced strains of Streptococcus pyogenes. Shown in FIG. 4 is a 3D diagram of base composition (axes A, G and C) of bioagent identifying amplicons obtained with primer pair number 14 (a precursor of primer pair number 348 which targets 16S rRNA). The diagram indicates that the experimentally determined base compositions of the clinical samples closely match the base compositions expected for Streptococcus pyogenes and are distinct from the expected base compositions of other organisms.

In addition to the identification of Streptococcus pyogenes, other potentially pathogenic organisms were identified concurrently. Mass spectral analysis of a sample whose nucleic acid was amplified by primer pair number 349 (SEQ ID NOs: 401:1156) exhibited signals of bioagent identifying amplicons with molecular masses that were found to correspond to analogous base compositions of bioagent identifying amplicons of Streptococcus pyogenes (A27 G32 C24 Ti 8), Neisseria meningitidis (A25 G27 C22 T18 Haemophilus influenzae (A28 G28 C25 T20) (see FIG. 5 and Table 7B). These organisms were present in a ratio of 4:5:20 as determined by comparison of peak heights with peak height of an internal PCR calibration standard as described in commonly owned U.S. Patent Application Ser. No: 60/545,425 which is incorporated herein by reference in its entirety.

Since certain division-wide primers that target housekeeping genes are designed to provide coverage of specific divisions of bacteria to increase the confidence level for identification of bacterial species, they are not expected to yield bioagent identifying amplicons for organisms outside of the specific divisions. For example, primer pair number 356 (SEQ ID NOs: 449:1380) primarily amplifies the nucleic acid of members of the classes Bacilli and Clostridia and is not expected to amplify proteobacteria such as Neisseria meningitidis and Haemophilus influenzae. As expected, analysis of the mass spectrum of amplification products obtained with primer pair number 356 does not indicate the presence of Neisseria meningitidis and Haemophilus influenzae but does indicate the presence of Streptococcus pyogenes (FIGS. 3 and 6, Table 7B). Thus, these primers or types of primers can confirm the absence of particular bioagents from a sample.

The 15 throat swabs from military recruits were found to contain a relatively small set of microbes in high abundance. The most common were Haemophilus influenza, Neisseria meningitides, and Streptococcus pyogenes. Staphylococcus epidermidis, Moraxella cattarhalis, Corynebacterium pseudodiphtheriticum, and Staphylococcus aureus were present in fewer samples. An equal number of samples from healthy volunteers from three different geographic locations, were identically analyzed. Results indicated that the healthy volunteers have bacterial flora dominated by multiple, commensal non-beta-hemolytic Streptococcal species, including the viridans group streptococci (S. parasangunis, S. vestibularis, S. mitis, S. oralis and S. pneumoniae; data not shown), and none of the organisms found in the military recruits were found in the healthy controls at concentrations detectable by mass spectrometry. Thus, the military recruits in the midst of a respiratory disease outbreak had a dramatically different microbial population than that experienced by the general population in the absence of epidemic disease.

Example 7 Triangulation Genotyping Analysis for Determination of emm-Type of Streptococcus pyogenes in Epidemic Surveillance

As a continuation of the epidemic surveillance investigation of Example 6, determination of sub-species characteristics (genotyping) of Streptococcus pyogenes, was carried out based on a strategy that generates strain-specific signatures according to the rationale of Multi-Locus Sequence Typing (MLST). In classic MLST analysis, internal fragments of several housekeeping genes are amplified and sequenced (Enright et al. Infection and Immunity, 2001, 69, 2416-2427). In classic MLST analysis, internal fragments of several housekeeping genes are amplified and sequenced. In the present investigation, bioagent identifying amplicons from housekeeping genes were produced using drill-down primers and analyzed by mass spectrometry. Since mass spectral analysis results in molecular mass, from which base composition can be determined, the challenge was to determine whether resolution of emm classification of strains of Streptococcus pyogenes could be determined.

For the purpose of development of a triangulation genotyping assay, an alignment was constructed of concatenated alleles of seven MLST housekeeping genes (glucose kinase (gki), glutamine transporter protein (gtr), glutamate racemase (murn), DNA mismatch repair protein (mutS), xanthine phosphoribosyl transferase (xpt), and acetyl-CoA acetyl transferase (yqiL)) from each of the 212 previously emm-typed strains of Streptococcus pyogenes. From this alignment, the number and location of primer pairs that would maximize strain identification via base composition was determined. As a result, 6 primer pairs were chosen as standard drill-down primers for determination of emm-type of Streptococcus pyogenes. These six primer pairs are displayed in Table 8. This drill-down set comprises primers with T modifications (note TMOD designation in primer names) which constitutes a functional improvement with regard to prevention of non-templated adenylation (vide supra) relative to originally selected primers which are displayed below in the same row. TABLE 8 Triangulation Genotyping Analysis Primer Pairs for Group A Streptococcus Drill-Down Primer Forward Primer Reverse Primer Pair No. Forward Primer Name (SEQ ID NO:) Reverse Primer Name (SEQ ID NO:) Target Gene 442 SP101_SPET11_358_387_TMOD_F 588 SP101_SPET11_448_473_TMOD_R 998 gki 80 SP101_SPET11_358_387_F 126 SP101_SPET11_448_473_TMOD_R 766 gki 443 SP101_SPET11_600_629_TMOD_F 348 SP101_SPET11_686_714_TMOD_R 1018 gtr 81 SP101_SPET11_600_629_F 62 SP101_SPET11_686_714_R 772 gtr 426 SP101_SPET11_1314_1336_TMOD_F 363 SP101_SPET11_1403_1431_TMOD_R 849 murI 86 SP101_SPET11_1314_1336_F 68 SP101_SPET11_1403_1431_R 711 murI 430 SP101_SPET11_1807_1835_TMOD_F 235 SP101_SPET11_1901_1927_TMOD_R 1439 mutS 90 SP101_SPET11_1807_1835_F 33 SP101_SPET11_1901_1927_R 1412 mutS 438 SP101_SPET11_3075_3103_TMOD_F 473 SP101_SPET11_3168_3196_TMOD_R 875 xpt 96 SP101_SPET11_3075_3103_F 108 SP101_SPET11_3168_3196_R 715 xpt 441 SP101_SPET11_3511_3535_TMOD_F 531 SP101_SPET11_3605_3629_TMOD_R 1294 yqiL 98 SP101_SPET11_3511_3535_F 116 SP101_SPET11_3605_3629_R 832 yqiL

The primers of Table 8 were used to produce bioagent identifying amplicons from nucleic acid present in the clinical samples. The bioagent identifying amplicons which were subsequently analyzed by mass spectrometry and base compositions corresponding to the molecular masses were calculated.

Of the 51 samples taken during the peak of the November/December 2002 epidemic (Table 9A-C rows 1-3), all except three samples were found to represent emm3, a Group A Streptococcus genotype previously associated with high respiratory virulence. The three outliers were from samples obtained from healthy individuals and probably represent non-epidemic strains. Archived samples (Tables 9A-C rows 5-13) from historical collections showed a greater heterogeneity of base compositions and emm types as would be expected from different epidemics occurring at different places and dates. The results of the mass spectrometry analysis and emm gene sequencing were found to be concordant for the epidemic and historical samples. TABLE 9A Base Composition Analysis of Bioagent Identifying Amplicons of Group A Streptococcus samples from Six Military Installations Obtained with Primer Pair Nos. 426 and 430 emm-type by murI mutS # of Mass emm-Gene Location (Primer Pair (Primer Pair Instances Spectrometry Sequencing (sample) Year No. 426) No. 430) 48  3  3 MCRD San 2002 A39 G25 C20 T34 A38 G27 C23 T33 2 6  6 Diego A40 G24 C20 T34 A38 G27 C23 T33 1 28  28 (Cultured) A39 G25 C20 T34 A38 G27 C23 T33 15  3 ND A39 G25 C20 T34 A38 G27 C23 T33 6 3  3 NHRC San 2003 A39 G25 C20 T34 A38 G27 C23 T33 3 5, 58  5 Diego- A40 G24 C20 T34 A38 G27 C23 T33 6 6  6 Archive A40 G24 C20 T34 A38 G27 C23 T33 1 11  11 (Cultured) A39 G25 C20 T34 A38 G27 C23 T33 3 12  12 A40 G24 C20 T34 A38 G26 C24 T33 1 22  22 A39 G25 C20 T34 A38 G27 C23 T33 3 25, 75  75 A39 G25 C20 T34 A38 G27 C23 T33 4 44/61, 82, 9 44/61 A40 G24 C20 T34 A38 G26 C24 T33 2 53, 91 91 A39 G25 C20 T34 A38 G27 C23 T33 1 2  2 Ft. 2003 A39 G25 C20 T34 A38 G27 C24 T32 2 3  3 Leonard A39 G25 C20 T34 A38 G27 C23 T33 1 4  4 Wood A39 G25 C20 T34 A38 G27 C23 T33 1 6  6 (Cultured) A40 G24 C20 T34 A38 G27 C23 T33 11  25 or 75 75 A39 G25 C20 T34 A38 G27 C23 T33 1 25, 75, 33, 75 A39 G25 C20 T34 A38 G27 C23 T33 34, 4, 52, 84 1 44/61 or 82 44/61 A40 G24 C20 T34 A38 G26 C24 T33 or 9 2 5 or 58  5 A40 G24 C20 T34 A38 G27 C23 T33 3 1  1 Ft. Sill 2003 A40 G24 C20 T34 A38 G27 C23 T33 2 3  3 (Cultured) A39 G25 C20 T34 A38 G27 C23 T33 1 4  4 A39 G25 C20 T34 A38 G27 C23 T33 1 28  28 A39 G25 C20 T34 A38 G27 C23 T33 1 3  3 Ft. 2003 A39 G25 C20 T34 A38 G27 C23 T33 1 4  4 Benning A39 G25 C20 T34 A38 G27 C23 T33 3 6  6 (Cultured) A40 G24 C20 T34 A38 G27 C23 T33 1 11  11 A39 G25 C20 T34 A38 G27 C23 T33 1 13   94** A40 G24 C20 T34 A38 G27 C23 T33 1 44/61 or 82 82 A40 G24 C20 T34 A38 G26 C24 T33 or 9 1 5 or 58 58 A40 G24 C20 T34 A38 G27 C23 T33 1 78 or 89 89 A39 G25 C20 T34 A38 G27 C23 T33 2 5 or 58 ND Lackland 2003 A40 G24 C20 T34 A38 G27 C23 T33 1 2 AFB A39 G25 C20 T34 A38 G27 C24 T32 1 81 or 90 (Throat A40 G24 C20 T34 A38 G27 C23 T33 1 78  Swabs) A38 G26 C20 T34 A38 G27 C23 T33   3*** No detection No detection No detection 7 3 ND MCRD San 2002 A39 G25 C20 T34 A38 G27 C23 T33 1 3 ND Diego No detection A38 G27 C23 T33 1 3 ND (Throat No detection No detection 1 3 ND Swabs) No detection No detection 2 3 ND No detection A38 G27 C23 T33 3 No detection ND No detection No detection

TABLE 9B Base Composition Analysis of Bioagent Identifying Amplicons of Group A Streptococcus samples from Six Military Installations Obtained with Primer Pair Nos. 438 and 441 emm-type by xpt yqiL # of Mass emm-Gene Location (Primer Pair (Primer Pair Instances Spectrometry Sequencing (sample) Year No. 438) No. 441) 48  3  3 MCRD San 2002 A30 G36 C20 T36 A40 G29 C19 T31 2 6  6 Diego A30 G36 C20 T36 A40 G29 C19 T31 1 28  28 (Cultured) A30 G36 C20 T36 A41 G28 C18 T32 15  3 ND A30 G36 C20 T36 A40 G29 C19 T31 6 3  3 NHRC San 2003 A30 G36 C20 T36 A40 G29 C19 T31 3 5, 58  5 Diego- A30 G36 C20 T36 A40 G29 C19 T31 6 6  6 Archive A30 G36 C20 T36 A40 G29 C19 T31 1 11  11 (Cultured) A30 G36 C20 T36 A40 G29 C19 T31 3 12  12 A30 G36 C19 T37 A40 G29 C19 T31 1 22  22 A30 G36 C20 T36 A40 G29 C19 T31 3 25, 75 75 A30 G36 C20 T36 A40 G29 C19 T31 4 44/61, 82, 9 44/61 A30 G36 C20 T36 A41 G28 C19 T31 2 53, 91 91 A30 G36 C19 T37 A40 G29 C19 T31 1 2  2 Ft. 2003 A30 G36 C20 T36 A40 G29 C19 T31 2 3  3 Leonard A30 G36 C20 T36 A40 G29 C19 T31 1 4  4 Wood A30 G36 C19 T37 A41 G28 C19 T31 1 6  6 (Cultured) A30 G36 C20 T36 A40 G29 C19 T31 11  25 or 75 75 A30 G36 C20 T36 A40 G29 C19 T31 1 25, 75, 33, 75 A30 G36 C19 T37 A40 G29 C19 T31 34, 4, 52, 84 1 44/61 or 82 44/61 A30 G36 C20 T36 A41 G28 C19 T31 or 9 2 5 or 58  5 A30 G36 C20 T36 A40 G29 C19 T31 3 1  1 Ft. Sill 2003 A30 G36 C19 T37 A40 G29 C19 T31 2 3  3 (Cultured) A30 G36 C20 T36 A40 G29 C19 T31 1 4  4 A30 G36 C19 T37 A41 G28 C19 T31 1 28  28 A30 G36 C20 T36 A41 G28 C18 T32 1 3  3 Ft. 2003 A30 G36 C20 T36 A40 G29 C19 T31 1 4  4 Benning A30 G36 C19 T37 A41 G28 C19 T31 3 6  6 (Cultured) A30 G36 C20 T36 A40 G29 C19 T31 1 11  11 A30 G36 C20 T36 A40 G29 C19 T31 1 13   94** A30 G36 C20 T36 A41 G28 C19 T31 1 44/61 or 82 82 A30 G36 C20 T36 A41 G28 C19 T31 or 9 1 5 or 58 58 A30 G36 C20 T36 A40 G29 C19 T31 1 78 or 89 89 A30 G36 C20 T36 A41 G28 C19 T31 2 5 or 58 ND Lackland 2003 A30 G36 C20 T36 A40 G29 C19 T31 1 2 AFB A30 G36 C20 T36 A40 G29 C19 T31 1 81 or 90 (Throat A30 G36 C20 T36 A40 G29 C19 T31 1 78  Swabs) A30 G36 C20 T36 A41 G28 C19 T31   3*** No detection No detection No detection 7 3 ND MCRD San 2002 A30 G36 C20 T36 A40 G29 C19 T31 1 3 ND Diego A30 G36 C20 T36 A40 G29 C19 T31 1 3 ND (Throat A30 G36 C20 T36 No detection 1 3 ND Swabs) No detection A40 G29 C19 T31 2 3 ND A30 G36 C20 T36 A40 G29 C19 T31 3 No detection ND No detection No detection

TABLE 9C Base Composition Analysis of Bioagent Identifying Amplicons of Group A Streptococcus samples from Six Military Installations Obtained with Primer Pair Nos. 438 and 441 emm-type by gki gtr # of Mass emm-Gene Location (Primer Pair ((Primer Pair Instances Spectrometry Sequencing (sample) Year No. 442) No. 443) 48  3  3 MCRD San 2002 A32 G35 C17 T32 A39 G28 C16 T32 2 6  6 Diego A31 G35 C17 T33 A39 G28 C15 T33 1 28  28 (Cultured) A30 G36 C17 T33 A39 G28 C16 T32 15  3 ND A32 G35 C17 T32 A39 G28 C16 T32 6 3  3 NHRC San 2003 A32 G35 C17 T32 A39 G28 C16 T32 3 5, 58  5 Diego- A30 G36 C20 T30 A39 G28 C15 T33 6 6  6 Archive A31 G35 C17 T33 A39 G28 C15 T33 1 11  11 (Cultured) A30 G36 C20 T30 A39 G28 C16 T32 3 12  12 A31 G35 C17 T33 A39 G28 C15 T33 1 22  22 A31 G35 C17 T33 A38 G29 C15 T33 3 25, 75 75 A30 G36 C17 T33 A39 G28 C15 T33 4 44/61, 82, 9 44/61 A30 G36 C18 T32 A39 G28 C15 T33 2 53, 91 91 A32 G35 C17 T32 A39 G28 C16 T32 1 2  2 Ft. 2003 A30 G36 C17 T33 A39 G28 C15 T33 2 3  3 Leonard A32 G35 C17 T32 A39 G28 C16 T32 1 4  4 Wood A31 G35 C17 T33 A39 G28 C15 T33 1 6  6 (Cultured) A31 G35 C17 T33 A39 G28 C15 T33 11  25 or 75 75 A30 G36 C17 T33 A39 G28 C15 T33 1 25, 75, 33, 75 A30 G36 C17 T33 A39 G28 C15 T33 34, 4, 52, 84 1 44/61 or 82 44/61 A30 G36 C18 T32 A39 G28 C15 T33 or 9 2 5 or 58  5 A30 G36 C20 T30 A39 G28 C15 T33 3 1  1 Ft. Sill 2003 A30 G36 C18 T32 A39 G28 C15 T33 2 3  3 (Cultured) A32 G35 C17 T32 A39 G28 C16 T32 1 4  4 A31 G35 C17 T33 A39 G28 C15 T33 1 28  28 A30 G36 C17 T33 A39 G28 C16 T32 1 3  3 Ft. 2003 A32 G35 C17 T32 A39 G28 C16 T32 1 4  4 Benning A31 G35 C17 T33 A39 G28 C15 T33 3 6  6 (Cultured) A31 G35 C17 T33 A39 G28 C15 T33 1 11  11 A30 G36 C20 T30 A39 G28 C16 T32 1 13   94** A30 G36 C19 T31 A39 G28 C15 T33 1 44/61 or 82 82 A30 G36 C18 T32 A39 G28 C15 T33 or 9 1 5 or 58 58 A30 G36 C20 T30 A39 G28 C15 T33 1 78 or 89 89 A30 G36 C18 T32 A39 G28 C15 T33 2 5 or 58 ND Lackland 2003 A30 G36 C20 T30 A39 G28 C15 T33 1 2 AFB A30 G36 C17 T33 A39 G28 C15 T33 1 81 or 90 (Throat A30 G36 C17 T33 A39 G28 C15 T33 1 78  Swabs) A30 G36 C18 T32 A39 G28 C15 T33   3*** No detection No detection No detection 7 3 ND MCRD San 2002 A32 G35 C17 T32 A39 G28 C16 T32 1 3 ND Diego No detection No detection 1 3 ND (Throat A32 G35 C17 T32 A39 G28 C16 T32 1 3 ND Swabs) A32 G35 C17 T32 No detection 2 3 ND A32 G35 C17 T32 No detection 3 No detection ND No detection No detection

Example 8 Design of Calibrant Polynucleotides based on Bioagent Identifying Amplicons for Identification of Species of Bacteria (Bacterial Bioagent Identifying Amplicons)

This example describes the design of 19 calibrant polynucleotides based on bacterial bioagent identifying amplicons corresponding to the primers of the broad surveillance set (Table 5) and the Bacillus anthracis drill-down set (Table 6).

Calibration sequences were designed to simulate bacterial bioagent identifying amplicons produced by the T modified primer pairs shown in Tables 5 and 6 (primer names have the designation “TMOD”). The calibration sequences were chosen as a representative member of the section of bacterial genome from specific bacterial species which would be amplified by a given primer pair. The model bacterial species upon which the calibration sequences are based are also shown in Table 10. For example, the calibration sequence chosen to correspond to an amplicon produced by primer pair no. 361 is SEQ ID NO: 1445. In Table 10, the forward (_F) or reverse (_R) primer name indicates the coordinates of an extraction representing a gene of a standard reference bacterial genome to which the primer hybridizes e.g.: the forward primer name 16S_EC_(—)713_(—)732_TMOD_F indicates that the forward primer hybridizes to residues 713-732 of the gene encoding 16S ribosomal RNA in an E. coli reference sequence (in this case, the reference sequence is an extraction consisting of residues 4033120-4034661 of the genomic sequence of E. coli K12 (GenBank gi number 16127994). Additional gene coordinate reference information is shown in Table 11. The designation “TMOD” in the primer names indicates that the 5′ end of the primer has been modified with a non-matched template T residue which prevents the PCR polymerase from adding non-templated adenosine residues to the 5′ end of the amplification product, an occurrence which may result in miscalculation of base composition from molecular mass data (vide supra).

The 19 calibration sequences described in Tables 10 and 11 were combined into a single calibration polynucleotide sequence (SEQ ID NO: 1464—which is herein designated a “combination calibration polynucleotide”) which was then cloned into a pCR®-Blunt vector (Invitrogen, Carlsbad, Calif.). This combination calibration polynucleotide can be used in conjunction with the primers of Tables 5 or 6 as an internal standard to produce calibration amplicons for use in determination of the quantity of any bacterial bioagent. Thus, for example, when the combination calibration polynucleotide vector is present in an amplification reaction mixture, a calibration amplicon based on primer pair 346 (16S rRNA) will be produced in an amplification reaction with primer pair 346 and a calibration amplicon based on primer pair 363 (rpoC) will be produced with primer pair 363. Coordinates of each of the 19 calibration sequences within the calibration polynucleotide (SEQ ID NO: 1464) are indicated in Table 11. TABLE 10 Bacterial Primer Pairs for Production of Bacterial Bioagent Identifying Amplicons and Corresponding Representative Calibration Sequences Forward Reverse Calibration Primer Primer Calibration Sequence Primer (SEQ ID (SEQ ID Sequence Model (SEQ ID Pair No. Forward Primer Name NO:) Reverse Primer Name NO:) Species NO:) 361 16S_EC_1090_1111_2_TMOD_F 697 16S_EC_1175_1196_TMOD_R 1398 Bacillus 1445 anthracis 346 16S_EC_713_732_TMOD_F 202 16S_EC_789_809_TMOD_R 1110 Bacillus 1446 anthracis 347 16S_EC_785_806_TMOD_F 560 16S_EC_880_897_TMOD_R 1278 Bacillus 1447 anthracis 348 16S_EC_960_981_TMOD_F 706 16S_EC_1054_1073_TMOD_R 895 Bacillus 1448 anthracis 349 23S_EC_1826_1843_TMOD_F 401 23S_EC_1906_1924_TMOD_R 1156 Bacillus 1449 anthracis 360 23S_EC_2646_2667_TMOD_F 409 23S_EC_2745_2765_TMOD_R 1434 Bacillus 1450 anthracis 350 CAPC_BA_274_303_TMOD_F 476 CAPC_BA_349_376_TMOD_R 1314 Bacillus 1451 anthracis 351 CYA_BA_1353_1379_TMOD_F 355 CYA_BA_1448_1467_TMOD_R 1423 Bacillus 1452 anthracis 352 INFB_EC_1365_1393_TMOD_F 687 INFB_EC_1439_1467_TMOD_R 1411 Bacillus 1453 anthracis 353 LEF_BA_756_781_TMOD_F 220 LEF_BA_843_872_TMOD_R 1394 Bacillus 1454 anthracis 356 RPLB_EC_650_679_TMOD_F 449 RPLB_EC_739_762_TMOD_R 1380 Clostridium 1455 botulinum 449 RPLB_EC_690_710_F 309 RPLB_EC_737_758_R 1336 Clostridium 1456 botulinum 359 RPOB_EC_1845_1866_TMOD_F 659 RPOB_EC_1909_1929_TMOD_R 1250 Yersinia 1457 Pestis 362 RPOB_EC_3799_3821_TMOD_F 581 RPOB_EC_3862_3888_TMOD_R 1325 Burkholderia 1458 mallei 363 RPOC_EC_2146_2174_TMOD_F 284 RPOC_EC_2227_2245_TMOD_R 898 Burkholderia 1459 mallei 354 RPOC_EC_2218_2241_TMOD_F 405 RPOC_EC_2313_2337_TMOD_R 1072 Bacillus 1460 anthracis 355 SSPE_BA_115_137_TMOD_F 255 SSPE_BA_197_222_TMOD_R 1402 Bacillus 1461 anthracis 367 TUFB_EC_957_979_TMOD_F 308 TUFB_EC_1034_1058_TMOD_R 1276 Burkholderia 1462 mallei 358 VALS_EC_1105_1124_TMOD_F 385 VALS_EC_1195_1218_TMOD_R 1093 Yersinia 1463 Pestis

TABLE 11 Primer Pair Gene Coordinate References and Calibration Polynucleotide Sequence Coordinates within the Combination Calibration Polynucleotide Coordinates of Gene Extraction Calibration Sequence in Bacterial Coordinates Reference GenBank GI Combination Calibration Gene and of Genomic or Plasmid No. of Genomic (G) or Primer Polynucleotide (SEQ ID Species Sequence Plasmid (P) Sequence Pair No. NO: 1464) 16S E. coli 4033120 . . . 4034661 16127994 (G) 346  16 . . . 109 16S E. coli 4033120 . . . 4034661 16127994 (G) 347  83 . . . 190 16S E. coli 4033120 . . . 4034661 16127994 (G) 348 246 . . . 353 16S E. coli 4033120 . . . 4034661 16127994 (G) 361 368 . . . 469 23S E. coli 4166220 . . . 4169123 16127994 (G) 349 743 . . . 837 23S E. coli 4166220 . . . 4169123 16127994 (G) 360 865 . . . 981 rpoB E. coli. 4178823 . . . 4182851 16127994 (G) 359 1591 . . . 1672 (complement strand) rpoB E. coli 4178823 . . . 4182851 16127994 (G) 362 2081 . . . 2167 (complement strand) rpoC E. coli 4182928 . . . 4187151 16127994 (G) 354 1810 . . . 1926 rpoC E. coli 4182928 . . . 4187151 16127994 (G) 363 2183 . . . 2279 infB E. coli 3313655 . . . 3310983 16127994 (G) 352 1692 . . . 1791 (complement strand) tufB E. coli 4173523 . . . 4174707 16127994 (G) 367 2400 . . . 2498 rplB E. coli 3449001 . . . 3448180 16127994 (G) 356 1945 . . . 2060 rplB E. coli 3449001 . . . 3448180 16127994 (G) 449 1986 . . . 2055 valS E. coli 4481405 . . . 4478550 16127994 (G) 358 1462 . . . 1572 (complement strand) capC 56074 . . . 55628  6470151 (P) 350 2517 . . . 2616 B. anthracis (complement strand) cya 156626 . . . 154288  4894216 (P) 351 1338 . . . 1449 B. anthracis (complement strand) lef 127442 . . . 129921  4894216 (P) 353 1121 . . . 1234 B. anthracis sspE 226496 . . . 226783 30253828 (G) 355 1007-1104 B. anthracis

Example 9 Use of a Calibration Polynucleotide for Determining the Quantity of Bacillus Anthracis in a Sample Containing a Mixture of Microbes

The process described in this example is shown in FIG. 2. The capC gene is a gene involved in capsule synthesis which resides on the pX02 plasmid of Bacillus anthracis. Primer pair number 350 (see Tables 10 and 11) was designed to identify Bacillus anthracis via production of a bacterial bioagent identifying amplicon. Known quantities of the combination calibration polynucleotide vector described in Example 8 were added to amplification mixtures containing bacterial bioagent nucleic acid from a mixture of microbes which included the Ames strain of Bacillus anthracis. Upon amplification of the bacterial bioagent nucleic acid and the combination calibration polynucleotide vector with primer pair no. 350, bacterial bioagent identifying amplicons and calibration amplicons were obtained and characterized by mass spectrometry. A mass spectrum measured for the amplification reaction is shown in FIG. 7. The molecular masses of the bioagent identifying amplicons provided the means for identification of the bioagent from which they were obtained (Ames strain of Bacillus anthracis) and the molecular masses of the calibration amplicons provided the means for their identification as well. The relationship between the abundance (peak height) of the calibration amplicon signals and the bacterial bioagent identifying amplicon signals provides the means of calculation of the copies of the pX02 plasmid of the Ames strain of Bacillus anthracis. Methods of calculating quantities of molecules based on internal calibration procedures are well known to those of ordinary skill in the art.

Averaging the results of 10 repetitions of the experiment described above, enabled a calculation that indicated that the quantity of Ames strain of Bacillus anthracis present in the sample corresponds to approximately 10 copies of pX02 plasmid.

Example 10 Triangulation Genotyping Analysis of Campylobacter Species

A series of triangulation genotyping analysis primers were designed as described in Example 1 with the objective of identification of different strains of Campylobacter jejuni. The primers are listed in Table 12 with the designation “CJST_CJ.” Housekeeping genes to which the primers hybridize and produce bioagent identifying amplicons include: tkt (transketolase), glyA (serine hydroxymethyltransferase), gltA (citrate synthase), aspA (aspartate ammonia lyase), glnA (glutamine synthase), pgm (phosphoglycerate mutase), and uncA (ATP synthetase alpha chain). TABLE 12 Campylobacter Genotyping Primer Pairs Primer Pair Forward Primer Reverse Primer No. Forward Primer Name (SEQ ID NO:) Reverse Primer Name (SEQ ID NO:) Target Gene 1053 CJST_CJ_1080_1110_F 681 CJST_CJ_1166_1198_R 1022 gltA 1047 CJST_CJ_584_616_F 315 CJST_CJ_663_692_R 1379 glnA 1048 CJST_CJ_360_394_F 346 CJST_CJ_442_476_R 955 aspA 1049 CJST_CJ_2636_2668_F 504 CJST_CJ_2753_2777_R 1409 tkt 1054 CJST_CJ_2060_2090_F 323 CJST_CJ_2148_2174_R 1068 pgm 1064 CJST_CJ_1680_1713_F 479 CJST_CJ_1795_1822_R 938 glyA

The primers were used to amplify nucleic acid from 50 food product samples provided by the USDA, 25 of which contained Campylobacter jejuni and 25 of which contained Campylobacter coli. Primers used in this study were developed primarily for the discrimination of Campylobacter jejuni clonal complexes and for distinguishing Campylobacter jejuni from Campylobacter coli. Finer discrimination between Campylobacter coli types is also possible by using specific primers targeted to loci where closely-related Campylobacter coli isolates demonstrate polymorphisms between strains. The conclusions of the comparison of base composition analysis with sequence analysis are shown in Tables 1 3A-C. TABLE 13A Results of Base Composition Analysis of 50 Campylobacter Samples with Drill-down MLST Primer Pair Nos: 1048 and 1047 Base Base Composition of Composition of MLST type or Bioagent Bioagent Clonal MLST Type Identifying Identifying Complex by or Clonal Amplicon Amplicon Base Complex by Obtained with Obtained with Isolate Composition Sequence Primer Pair No: Primer Pair Group Species origin analysis analysis Strain 1048 (aspA) No: 1047 (glnA) J-1 C. jejuni Goose ST 690/ ST 991 RM3673 A30 G25 C16 T46 A47 G21 C16 T25 692/707/991 J-2 C. jejuni Human Complex ST 356, RM4192 A30 G25 C16 T46 A48 G21 C17 T23 206/48/353 complex 353 J-3 C. jejuni Human Complex ST 436 RM4194 A30 G25 C15 T47 A48 G21 C18 T22 354/179 J-4 C. jejuni Human Complex 257 ST 257, RM4197 A30 G25 C16 T46 A48 G21 C18 T22 complex 257 J-5 C. jejuni Human Complex 52 ST 52, RM4277 A30 G25 C16 T46 A48 G21 C17 T23 complex 52 J-6 C. jejuni Human Complex 443 ST 51, RM4275 A30 G25 C15 T47 A48 G21 C17 T23 complex RM4279 A30 G25 C15 T47 A48 G21 C17 T23 443 J-7 C. jejuni Human Complex 42 ST 604, RM1864 A30 G25 C15 T47 A48 G21 C18 T22 complex 42 J-8 C. jejuni Human Complex ST 362, RM3193 A30 G25 C15 T47 A48 G21 C18 T22 42/49/362 complex 362 J-9 C. jejuni Human Complex ST 147, RM3203 A30 G25 C15 T47 A47 G21 C18 T23 45/283 Complex 45 C. jejuni Human Consistent ST 828 RM4183 A31 G27 C20 T39 A48 G21 C16 T24 C-1 C. coli with 74 ST 832 RM1169 A31 G27 C20 T39 A48 G21 C16 T24 closely ST 1056 RM1857 A31 G27 C20 T39 A48 G21 C16 T24 Poultry related ST 889 RM1166 A31 G27 C20 T39 A48 G21 C16 T24 sequence ST 829 RM1182 A31 G27 C20 T39 A48 G21 C16 T24 types (none ST 1050 RM1518 A31 G27 C20 T39 A48 G21 C16 T24 belong to a ST 1051 RM1521 A31 G27 C20 T39 A48 G21 C16 T24 clonal ST 1053 RM1523 A31 G27 C20 T39 A48 G21 C16 T24 complex) ST 1055 RM1527 A31 G27 C20 T39 A48 G21 C16 T24 ST 1017 RM1529 A31 G27 C20 T39 A48 G21 C16 T24 ST 860 RM1840 A31 G27 C20 T39 A48 G21 C16 T24 ST 1063 RM2219 A31 G27 C20 T39 A48 G21 C16 T24 ST 1066 RM2241 A31 G27 C20 T39 A48 G21 C16 T24 ST 1067 RM2243 A31 G27 C20 T39 A48 G21 C16 T24 ST 1068 RM2439 A31 G27 C20 T39 A48 G21 C16 T24 Swine ST 1016 RM3230 A31 G27 C20 T39 A48 G21 C16 T24 ST 1069 RM3231 A31 G27 C20 T39 A48 G21 C16 T24 ST 1061 RM1904 A31 G27 C20 T39 A48 G21 C16 T24 Unknown ST 825 RM1534 A31 G27 C20 T39 A48 G21 C16 T24 ST 901 RM1505 A31 G27 C20 T39 A48 G21 C16 T24 C-2 C. coli Human ST 895 ST 895 RM1532 A31 G27 C19 T40 A48 G21 C16 T24 C-3 C. coli Poultry Consistent ST 1064 RM2223 A31 G27 C20 T39 A48 G21 C16 T24 with 63 ST 1082 RM1178 A31 G27 C20 T39 A48 G21 C16 T24 closely ST 1054 RM1525 A31 G27 C20 T39 A48 G21 C16 T24 related ST 1049 RM1517 A31 G27 C20 T39 A48 G21 C16 T24 Marmoset sequence ST 891 RM1531 A31 G27 C20 T39 A48 G21 C16 T24 types (none belong to a clonal complex)

TABLE 13B Results of Base Composition Analysis of 50 Campylobacter Samples with Drill- down MLST Primer Pair Nos: 1053 and 1064 Base Base Composition of Composition of MLST type or Bioagent Bioagent Clonal MLST Type Identifying Identifying Complex by or Clonal Amplicon Amplicon Base Complex by Obtained with Obtained with Isolate Composition Sequence Primer Pair Primer Pair Group Species origin analysis analysis Strain No: 1053 (gltA) No: 1064 (glyA) J-1 C. jejuni Goose ST 690/ ST 991 RM3673 A24 G25 C23 T47 A40 G29 C29 T45 692/707/991 J-2 C. jejuni Human Complex ST 356, RM4192 A24 G25 C23 T47 A40 G29 C29 T45 206/48/353 complex 353 J-3 C. jejuni Human Complex ST 436 RM4194 A24 G25 C23 T47 A40 G29 C29 T45 354/179 J-4 C. jejuni Human Complex 257 ST 257, RM4197 A24 G25 C23 T47 A40 G29 C29 T45 complex 257 J-5 C. jejuni Human Complex 52 ST 52, RM4277 A24 G25 C23 T47 A39 G30 C26 T48 complex 52 J-6 C. jejuni Human Complex 443 ST 51, RM4275 A24 G25 C23 T47 A39 G30 C28 T46 complex RM4279 A24 G25 C23 T47 A39 G30 C28 T46 443 J-7 C. jejuni Human Complex 42 ST 604, RM1864 A24 G25 C23 T47 A39 G30 C26 T48 complex 42 J-8 C. jejuni Human Complex ST 362, RM3193 A24 G25 C23 T47 A38 G31 C28 T46 42/49/362 complex 362 J-9 C. jejuni Human Complex ST 147, RM3203 A24 G25 C23 T47 A38 G31 C28 T46 45/283 Complex 45 C. jejuni Human Consistent ST 828 RM4183 A23 G24 C26 T46 A39 G30 C27 T47 C-1 C. coli with 74 ST 832 RM1169 A23 G24 C26 T46 A39 G30 C27 T47 closely ST 1056 RM1857 A23 G24 C26 T46 A39 G30 C27 T47 Poultry related ST 889 RM1166 A23 G24 C26 T46 A39 G30 C27 T47 sequence ST 829 RM1182 A23 G24 C26 T46 A39 G30 C27 T47 types (none ST 1050 RM1518 A23 G24 C26 T46 A39 G30 C27 T47 belong to a ST 1051 RM1521 A23 G24 C26 T46 A39 G30 C27 T47 clonal ST 1053 RM1523 A23 G24 C26 T46 A39 G30 C27 T47 complex) ST 1055 RM1527 A23 G24 C26 T46 A39 G30 C27 T47 ST 1017 RM1529 A23 G24 C26 T46 A39 G30 C27 T47 ST 860 RM1840 A23 G24 C26 T46 A39 G30 C27 T47 ST 1063 RM2219 A23 G24 C26 T46 A39 G30 C27 T47 ST 1066 RM2241 A23 G24 C26 T46 A39 G30 C27 T47 ST 1067 RM2243 A23 G24 C26 T46 A39 G30 C27 T47 ST 1068 RM2439 A23 G24 C26 T46 A39 G30 C27 T47 Swine ST 1016 RM3230 A23 G24 C26 T46 A39 G30 C27 T47 ST 1069 RM3231 A23 G24 C26 T46 NO DATA ST 1061 RM1904 A23 G24 C26 T46 A39 G30 C27 T47 Unknown ST 825 RM1534 A23 G24 C26 T46 A39 G30 C27 T47 ST 901 RM1505 A23 G24 C26 T46 A39 G30 C27 T47 C-2 C. coli Human ST 895 ST 895 RM1532 A23 G24 C26 T46 A39 G30 C27 T47 C-3 C. coli Poultry Consistent ST 1064 RM2223 A23 G24 C26 T46 A39 G30 C27 T47 with 63 ST 1082 RM1178 A23 G24 C26 T46 A39 G30 C27 T47 closely ST 1054 RM1525 A23 G24 C25 T47 A39 G30 C27 T47 related ST 1049 RM1517 A23 G24 C26 T46 A39 G30 C27 T47 Marmoset sequence ST 891 RM1531 A23 G24 C26 T46 A39 G30 C27 T47 types (none belong to a clonal complex)

TABLE 13C Results of Base Composition Analysis of 50 Campylobacter Samples with Drill- down MLST Primer Pair Nos: 1054 and 1049 Base Base Composition of Composition of MLST type or Bioagent Bioagent Clonal MLST Type Identifying Identifying Complex by or Clonal Amplicon Amplicon Base Complex by Obtained with Obtained with Isolate Composition Sequence Primer Pair No: Primer Pair Group Species origin analysis analysis Strain 1054 (pgm) No: 1049 (tkt) J-1 C. jejuni Goose ST 690/ ST 991 RM3673 A26 G33 C18 T38 A41 G28 C35 T38 692/707/991 J-2 C. jejuni Human Complex ST 356, RM4192 A26 G33 C19 T37 A41 G28 C36 T37 206/48/353 complex 353 J-3 C. jejuni Human Complex ST 436 RM4194 A27 G32 C19 T37 A42 G28 C36 T36 354/179 J-4 C. jejuni Human Complex 257 ST 257, RM4197 A27 G32 C19 T37 A41 G29 C35 T37 complex 257 J-5 C. jejuni Human complex 52 ST 52, RM4277 A26 G33 C18 T38 A41 G28 C36 T37 complex 52 J-6 C. jejuni Human Complex 443 ST 51, RM4275 A27 G31 C19 T38 A41 G28 C36 T37 complex RM4279 A27 G31 C19 T38 A41 G28 C36 T37 443 J-7 C. jejuni Human Complex 42 ST 604, RM1864 A27 G32 C19 T37 A42 G28 C35 T37 complex 42 J-8 C. jejuni Human Complex ST 362, RM3193 A26 G33 C19 T37 A42 G28 C35 T37 42/49/362 complex 362 J-9 C. jejuni Human Complex ST 147, RM3203 A28 G31 C19 T37 A43 G28 C36 T35 45/283 Complex 45 C. jejuni Human Consistent ST 828 RM4183 A27 G30 C19 T39 A46 G28 C32 T36 C-1 C. coli with 74 ST 832 RM1169 A27 G30 C19 T39 A46 G28 C32 T36 closely ST 1056 RM1857 A27 G30 C19 T39 A46 G28 C32 T36 Poultry related ST 889 RM1166 A27 G30 C19 T39 A46 G28 C32 T36 sequence ST 829 RM1182 A27 G30 C19 T39 A46 G28 C32 T36 types (none ST 1050 RM1518 A27 G30 C19 T39 A46 G28 C32 T36 belong to a ST 1051 RM1521 A27 G30 C19 T39 A46 G28 C32 T36 clonal ST 1053 RM1523 A27 G30 C19 T39 A46 G28 C32 T36 complex) ST 1055 RM1527 A27 G30 C19 T39 A46 G28 C32 T36 ST 1017 RM1529 A27 G30 C19 T39 A46 G28 C32 T36 ST 860 RM1840 A27 G30 C19 T39 A46 G28 C32 T36 ST 1063 RM2219 A27 G30 C19 T39 A46 G28 C32 T36 ST 1066 RM2241 A27 G30 C19 T39 A46 G28 C32 T36 ST 1067 RM2243 A27 G30 C19 T39 A46 G28 C32 T36 ST 1068 RM2439 A27 G30 C19 T39 A46 G28 C32 T36 Swine ST 1016 RM3230 A27 G30 C19 T39 A39 G30 C27 T47 ST 1069 RM3231 A27 G30 C19 T39 A46 G28 C32 T36 ST 1061 RM1904 A27 G30 C19 T39 A46 G28 C32 T36 Unknown ST 825 RM1534 A27 G30 C19 T39 A46 G28 C32 T36 ST 901 RM1505 A27 G30 C19 T39 A46 G28 C32 T36 C-2 C. coli Human ST 895 ST 895 RM1532 A27 G30 C19 T39 A46 G28 C32 T36 C-3 C. coli Poultry Consistent ST 1064 RM2223 A27 G30 C19 T39 A46 G28 C32 T36 with 63 ST 1082 RM1178 A27 G30 C19 T39 A46 G28 C32 T36 closely ST 1054 RM1525 A27 G30 C19 T39 A46 G28 C32 T36 related ST 1049 RM1517 A27 G30 C19 T39 A46 G28 C32 T36 Marmoset sequence ST 891 RM1531 A27 G30 C19 T39 A46 G28 C32 T36 types (none belong to a clonal complex)

The base composition analysis method was successful in identification of 12 different strain groups. Campylobacter jejuni and Campylobacter coli are generally differentiated by all loci. Ten clearly differentiated Campylobacter jejuni isolates and 2 major Campylobacter coli groups were identified even though the primers were designed for strain typing of Campylobacter jejuni. One isolate (RM4183) which was designated as Campylobacter jejuni was found to group with Campylobacter coli and also appears to actually be Campylobacter coli by full MLST sequencing.

Example 11 Identification of Acinetobacter baumannii Using Broad Range Survey and Division-Wide Primers in Epidemiological Surveillance

To test the capability of the broad range survey and division-wide primer sets of Table 5 in identification of Acinetobacter species, 183 clinical samples were obtained from individuals participating in, or in contact with individuals participating in Operation Iraqi Freedom (including US service personnel, US civilian patients at the Walter Reed Army Institute of Research (WRAIR), medical staff, Iraqi civilians and enemy prisoners. In addition, 34 environmental samples were obtained from hospitals in Iraq, Kuwait, Germany, the United States and the USNS Comfort, a hospital ship.

Upon amplification of nucleic acid obtained from the clinical samples, primer pairs 346-349, 360, 361, 354, 362 and 363 (Table 5) all produced bacterial bioagent amplicons which identified Acinetobacter baumannii in 215 of 217 samples. The organism Klebsiella pneumoniae was identified in the remaining two samples. In addition, 14 different strain types (containing single nucleotide polymorphisms relative to a reference strain of Acinetobacter baumannii) were identified and assigned arbitrary numbers from 1 to 14. Strain type 1 was found in 134 of the sample isolates and strains 3 and 7 were found in 46 and 9 of the isolates respectively.

The epidemiology of strain type 7 of Acinetobacter baumannii was investigated. Strain 7 was found in 4 patients and 5 environmental samples (from field hospitals in Iraq and Kuwait). The index patient infected with strain 7 was a pre-war patient who had a traumatic amputation in March of 2003 and was treated at a Kuwaiti hospital. The patient was subsequently transferred to a hospital in Germany and then to WRAIR. Two other patients from Kuwait infected with strain 7 were found to be non-infectious and were not further monitored. The fourth patient was diagnosed with a strain 7 infection in September of 2003 at WRAIR. Since the fourth patient was not related involved in Operation Iraqi Freedom, it was inferred that the fourth patient was the subject of a nosocomial infection acquired at WRAIk as a result of the spread of strain 7 from the index patient.

The epidemiology of strain type 3 of Acinetobacter baumannii was also investigated. Strain type 3 was found in 46 samples, all of which were from patients (US service members, Iraqi civilians and enemy prisoners) who were treated on the USNS Comfort hospital ship and subsequently returned to Iraq or Kuwait. The occurrence of strain type 3 in a single locale may provide evidence that at least some of the infections at that locale were a result of nosocomial infections.

This example thus illustrates an embodiment of the present invention wherein the methods of analysis of bacterial bioagent identifying amplicons provide the means for epidemiological surveillance.

Example 12 Selection and Use of Triangulation Genotyping Analysis Primer Pairs for Acinetobacter baumanii

To combine the power of high-throughput mass spectrometric analysis of bioagent identifying amplicons with the sub-species characteristic resolving power provided by triangulation genotyping analysis, an additional 21 primer pairs were selected based on analysis of housekeeping genes of the genus Acinetobacter. Genes to which the drill-down triangulation genotyping analysis primers hybridize for production of bacterial bioagent identifying amplicons include anthranilate synthase component I (trpE), adenylate kinase (adk), adenine glycosylase (mutY), fumarate hydratase (fumC), and pyrophosphate phospho-hydratase (ppa). These 21 primer pairs are indicated with reference to sequence listings in Table 14. Primer pair numbers 1151-1154 hybridize to and amplify segments of trpE. Primer pair numbers 1155-1157 hybridize to and amplify segments of adk. Primer pair numbers 1158-1164 hybridize to and amplify segments of mutY. Primer pair numbers 1165-1170 hybridize to and amplify segments of fumC. Primer pair number 1171 hybridizes to and amplifies a segment of ppa. Primer pair numbers: 2846-2848 hybridize to and amplify segments of the parC gene of DNA topoisomerase which include a codon known to confer quinolone drug resistance upon sub-types of Acinetobacter baumannii. Primer pair numbers 2852-2854 hybridize to and amplify segments of the gyrA gene of DNA gyrase which include a codon known to confer quinolone drug resistance upon sub-types of Acinetobacter baumannii. Primer pair numbers 2922 and 2972 are speciating primers which are useful for identifying different species members of the genus Acinetobacter. The primer names given in Table 14A (with the exception of primer pair numbers 2846-2848, 2852-2854) indicate the coordinates to which the primers hybridize to a reference sequence which comprises a concatenation of the genes TrpE, efp (elongation factor p), adk, mutT, fumC, and ppa. For example, the forward primer of primer pair 1151 is named AB_MLST-11-OIF007_(—)62_(—)91_F because it hybridizes to the Acinetobacter primer reference sequence of strain type 11 in sample 007 of Operation Iraqi Freedom (OIF) at positions 62 to 91. DNA was sequenced from strain type 11 and from this sequence data and an artificial concatenated sequence of partial gene extractions was assembled for use in design of the triangulation genotyping analysis primers. The stretches of arbitrary residues “N”s in the concatenated sequence were added for the convenience of separation of the partial gene extractions (40N for AB_MLST (SEQ ID NO: 1444)).

The hybridization coordinates of primer pair numbers 2846-2848 are with respect to GenBank Accession number X95819. The hybridization coordinates of primer pair numbers 2852-2854 are with respect to GenBank Accession number AY642140. Sequence residue “I” appearing in the forward and reverse primers of primer pair number 2972 represents inosine. TABLE 14A Triangulation Genotyping Analysis Primer Pairs for Identification of Sub-species characteristics (Strain Type) of Members of the Bacterial Genus Acinetobacter Primer Forward Primer Reverse Primer Pair No. Forward Primer Name (SEQ ID NO:) Reverse Primer Name (SEQ ID NO:) 1151 AB_MLST-11-OIF007_62_91_F 454 AB_MLST-11-OIF007_169_203_R 1418 1152 AB_MLST-11-OIF007_185_214_F 243 AB_MLST-11-OIF007_291_324_R 969 1153 AB_MLST-11-OIF007_260_289_F 541 AB_MLST-11-OIF007_364_393_R 1400 1154 AB_MLST-11-OIF007_206_239_F 436 AB_MLST-11-OIF007_318_344_R 1036 1155 AB_MLST-11-OIF007_522_552_F 378 AB_MLST-11-OIF007_587_610_R 1392 1156 AB_MLST-11-OIF007_547_571_F 250 AB_MLST-11-OIF007_656_686_R 902 1157 AB_MLST-11-OIF007_601_627_F 256 AB_MLST-11-OIF007_710_736_R 881 1158 AB_MLST-11-OIF007_1202_1225_F 384 AB_MLST-11-OIF007_1266_1296_R 878 1159 AB_MLST-11-OIF007_1202_1225_F 384 AB_MLST-11-OIF007_1299_1316_R 1199 1160 AB_MLST-11-OIF007_1234_1264_F 694 AB_MLST-11-OIF007_1335_1362_R 1215 1161 AB_MLST-11-OIF007_1327_1356_F 225 AB_MLST-11-OIF007_1422_1448_R 1212 1162 AB_MLST-11-OIF007_1345_1369_F 383 AB_MLST-11-OIF007_1470_1494_R 1083 1163 AB_MLST-11-OIF007_1351_1375_F 662 AB_MLST-11-OIF007_1470_1494_R 1083 1164 AB_MLST-11-OIF007_1387_1412_F 422 AB_MLST-11-OIF007_1470_1494_R 1083 1165 AB_MLST-11-OIF007_1542_1569_F 194 AB_MLST-11-OIF007_1656_1680_R 1173 1166 AB_MLST-11-OIF007_1566_1593_F 684 AB_MLST-11-OIF007_1656_1680_R 1173 1167 AB_MLST-11-OIF007_1611_1638_F 375 AB_MLST-11-OIF007_1731_1757_R 890 1168 AB_MLST-11-OIF007_1726_1752_F 182 AB_MLST-11-OIF007_1790_1821_R 1195 1169 AB_MLST-11-OIF007_1792_1826_F 656 AB_MLST-11-OIF007_1876_1909_R 1151 1170 AB_MLST-11-OIF007_1792_1826_F 656 AB_MLST-11-OIF007_1895_1927_R 1224 1171 AB_MLST-11-OIF007_1970_2002_F 618 AB_MLST-11-OIF007_2097_2118_R 1157 2846 PARC_X95819_33_58_F 302 PARC_X95819_121_153_R 852 2847 PARC_X95819_33_58_F 199 PARC_X95819_157_178_R 889 2848 PARC_X95819_33_58_F 596 PARC_X95819_97_128_R 1169 2852 GYRA_AY642140_−1_24_F 150 GYRA_AY642140_71_100_R 1242 2853 GYRA_AY642140_26_54_F 166 GYRA_AY642140_121_146_R 1069 2854 GYRA_AY642140_26_54_F 166 GYRA_AY642140_58_89_R 1168 2922 AB_MLST-11-OIF007_991_1018_F 583 AB_MLST-11-OIF007_1110_1137_R 923 2972 AB_MLST-11-OIF007_1007_1034_F 592 AB_MLST-11-OIF007_1126_1153_R 924

TABLE 14B Triangulation Genotyping Analysis Primer Pairs for Identification of Sub-species characteristics (Strain Type) of Members of the Bacterial Genus Acinetobacter Forward Reverse Primer Primer Primer Pair No. (SEQ ID NO:) SEQUENCE (SEQ ID NO: SEQUENCE 1151 454 TGAGATTGCTGAACATTTAATGCTGATTGA 1418 TTGTACATTTGAAACAATATGCATGACATGTGAAT 1152 243 TATTGTTTCAAATGTACAAGGTGAAGTGCG  969 TCACAGGTTCACTTCATCAATAATTTCCATTGC 1153 541 TGGAACGTTATCAGGTGCCCCAAAAATTCG 1400 TTGCAATCGACATATCCATTTCACCATGCC 1154 436 TGAAGTGCGTGATGATATCGATGCACTTGATGTA 1036 TCCGCCAAAAACTCCCCTTTTCACAGG 1155 378 TCGGTTTAGTAAAAGAACGTATTGCTCAACC 1392 TTCTGCTTGAGGAATAGTGCGTGG 1156 250 TCAACCTGACTGCGTGAATGGTTGT  902 TACGTTCTACGATTTCTTCATCAGGTACATC 1157 256 TCAAGCAGAAGCTTTGGAAGAAGAAGG  881 TACAACGTGATAAACACGACCAGAAGC 1158 384 TCGTGCCCGCAATTTGCATAAAGC  878 TAATGCCGGGTAGTGCAATCCATTCTTCTAG 1159 384 TCGTGCCCGCAATTTGCATAAAGC 1199 TGCACCTGCGGTCGAGCG 1160 694 TTGTAGCACAGCAAGGCAAATTTCCTCAAAC 1215 TGCCATCCATAATCACGCCATACTGACG 1161 225 TAGGTTTACGTCAGTATGGCGTGATTATGG 1212 TGCCAGTTTCCACATTTCACGTTCGTG 1162 383 TCGTGATTATGGATGGCAACGTGAA 1083 TCGCTTGAGTGTACTGATGATTGCG 1163 662 TTATGGATGGCAACGTGAAACGCGT 1083 TCGCTTGAGTGTAGTCATGATTGCG 1164 422 TCTTTGCCATTGAAGATGACTTAAGC 1083 TCGCTTGAGTGTAGTCATGATTGCG 1165 194 TACTAGCGGTAAGCTTAAACAAGATTGC 1173 TGAGTCGGGTTCACTTTACCTGGCA 1166 684 TTGCCAATGATATTCGTTGGTTAGCAAG 1173 TGAGTCGGGTTCACTTTACCTGGCA 1167 375 TCGGCGAAATCCGTATTCCTGAAAATGA  890 TACCGGAAGCACCAGCGACATTAATAG 1168 182 TACCACTATTAATGTCGCTGGTGCTTC 1195 TGCAACTGAATAGATTGCAGTAAGTTATAAGC 1169 656 TTATAACTTACTGCAATCTATTCAGTTGCTTGGT 1151 TGAATTATGCAAGAAGTGATCAATTTTCTCACGA G 1170 656 TTATAACTTACTGCAATCTATTCAGTTGCTTGGT 1224 TGCCGTAACTAACATAAGAGAATTATGCAAGAA G 1171 618 TGGTTATGTACCAAATACTTTGTCTGAAGATGG 1157 TGACGGCATCGATACCACCGTC 2846 302 TCCAAAAAAATCAGCGCGTACAGTGG  852 TAAAGGATAGCGGTAACTAAATGGCTGAGCCAT 2847 199 TACTTGGTAAATACCACCCACATGGTGA  889 TACCCCAGTTCCCCTGACCTTC 2848 596 TGGTAAATACCACCCACATGGTGAC 1169 TGAGCCATGAGTACCATGGCTTCATAACATGC 2852 150 TAAATCTGCCCGTGTCGTCGGTGAC 1242 TGCTAAAGTCTTGAGCCATACGAACAATGG 2853 166 TAATCGGTAAATATCACCCGCATGGTGAC 1069 TCGATCGAACCGAAGTTACCCTGACC 2854 166 TAATCGGTAAATATCACCCGCATGGTGAC 1168 TGAGCCATACGAACAATGGTTTCATAAACAGC 2922 583 TGGGCGATGCTGCGAAATGGTTAAAAGA  923 TAGTATCACCACGTACACCCGCATCAGT 2972 592 TGGGIGATGCTGCIAAATGGTTAAAAGA  924 TAGTATCACCACGTACICCIGGATCAGT

Analysis of bioagent identifying amplicons obtained using the primers of Table 14B for over 200 samples from Operation Iraqi Freedom resulted in the identification of 50 distinct strain type clusters. The largest cluster, designated strain type 11 (ST11) includes 42 sample isolates, all of which were obtained from US service personnel and Iraqi civilians treated at the 28^(th) Combat Support Hospital in Baghdad. Several of these individuals were also treated on the hospital ship USNS Comfort. These observations are indicative of significant epidemiological correlation/linkage.

All of the sample isolates were tested against a broad panel of antibiotics to characterize their antibodies resistance profiles. As an example of a representative result from antibiotic susceptibility testing, ST11 was found to consist of four different clusters of isolates, each with a varying degree of sensitivity/resistance to the various antibiotics tested which included penicillins, extended spectrum penicillins, cephalosporins, carbepenem, protein synthesis inhibitors, nucleic acid synthesis inhibitors, anti-metabolites, and anti-cell membrane antibiotics. Thus, the genotyping power of bacterial bioagent identifying amplicons, particularly drill-down bacterial bioagent identifying amplicons, has the potential to increase the understanding of the transmission of infections in combat casualties, to identify the source of infection in the environment, to track hospital transmission of nosocomial infections, and to rapidly characterize drug-resistance profiles which enable development of effective infection control measures on a time-scale previously not achievable.

Example 13 Triangulation Genotyping Analysis and Codon Analysis of Acinetobacter baumannii Samples from Two Health Care Facilities

In this investigation, 88 clinical samples were obtained from Walter Reed Hospital and 95 clinical samples were obtained from Northwestern Medical Center. All samples from both healthcare facilities were suspected of containing sub-types of Acinetobacter baumannii, at least some of which were expected to be resistant to quinolone drugs. Each of the 183 samples was analyzed by the method of the present invention. DNA was extracted from each of the samples and amplified with eight triangulation genotyping analysis primer pairs represented by primer pair numbers: 1151, 1156, 1158, 1160, 1165, 1167, 1170, and 1171. The DNA was also amplified with speciating primer pair number 2922 and codon analysis primer pair numbers 2846-2848 which interrogate a codon present in the parC gene, and primer pair numbers 2852-2854 which bracket a codon present in the gyrA gene. The parC and gyrA codon mutations are both responsible for causing drug resistance in Acinetobacter baumannii. During evolution of drug resistant strains, the gyrA mutation usually occurs before the parC mutation. Amplification products were measured by ESI-TOF mass spectrometry as indicated in Example 4. The base compositions of the amplification products were calculated from the average molecular masses of the amplification products and are shown in Tables 15-18. The entries in each of the tables are grouped according to strain type number, which is an arbitrary number assigned to Acinetobacter baumannii strains in the order of observance beginning from the triangulation genotyping analysis OIF genotyping study described in Example 12. For example, strain type 11 which appears in samples from the Walter Reed Hospital is the same strain as the strain type 11 mentioned in Example 12. Ibis# refers to the order in which each sample was analyzed. Isolate refers to the original sample isolate numbering system used at the location from which the samples were obtained (either Walter Reed Hospital or Northwestern Medical Center). ST=strain type. ND=not detected. Base compositions highlighted with bold type indicate that the base composition is a unique base composition for the amplification product obtained with the pair of primers indicated. TABLE 15A Base Compositions of Amplification Products of 88 A. baumannii Samples Obtained from Walter Reed Hospital and Amplified with Codon Analysis Primer Pairs Targeting the gyrA Gene PP No: 2852 PP No: 2853 PP No: 2854 Species Ibis# Isolate ST gyrA gyrA gyrA A. baumannii 20 1082 1 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii 13  854 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 22 1162 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 27 1230 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 31 1367 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 37 1459 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 55 1700 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 64 1777 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 73 1861 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 74 1877 10 ND A29G28C21T43 A17G13C13T21 A. baumannii 86 1972 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  3  684 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  6  720 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  7  726 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 19 1079 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 21 1123 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 23 1188 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 33 1417 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 34 1431 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 38 1496 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 40 1523 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 42 1640 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 50 1666 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 51 1668 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 52 1695 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 65 1781 11 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 44 1649 12 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii   49A   1658.1 12 A25G23C22T31 A29G28C21T43 A17G13C13T21 A. baumannii   49B   1658.2 12 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 56 1707 12 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 80 1893 12 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  5  693 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  8  749 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 10  839 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 14  865 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 16  888 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 29 1326 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 35 1440 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 41 1524 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 46 1652 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 47 1653 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 48 1657 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 57 1709 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 61 1727 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 63 1762 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 67 1806 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 75 1881 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 77 1886 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  1  649 46 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  2  653 46 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 39 1497 16 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 24 1198 15 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 28 1243 15 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 43 1648 15 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 62 1746 15 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii  4  689 15 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 68 1822 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 69   1823A 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 70   1823B 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 71 1826 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 72 1860 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 81 1924 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 82 1929 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 85 1966 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 11  841 3 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii 32 1415 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 45 1651 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 54 1697 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 58 1712 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 60 1725 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 66 1802 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 76 1883 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 78 1891 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 79 1892 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 83 1947 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 84 1964 24 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 53 1696 24 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii 36 1458 49 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 59 1716 9 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii  9  805 30 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii 18  967 39 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii 30 1322 48 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. baumannii 26 1218 50 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. sp. 13TU 15  875 A1 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. sp. 13TU 17  895 A1 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. sp. 3 12  853 B7 A25G22C22T32 A30G29C22T40 A17G13C14T20 A. johnsonii 25 1202 NEW1 A25G22C22T32 A30G29C22T40 A17G13C14T20 A. sp. 2082 87 2082 NEW2 A25G22C22T32 A31G28C22T40 A17G13C14T20

TABLE 15B Base Compositions Determined from A. baumannii DNA Samples Obtained from Walter Reed Hospital and Amplified with Codon Analysis Primer Pairs Targeting the parC Gene PP No: 2846 PP No: 2847 PP No: 2848 Species Ibis# Isolate ST parC parC parC A. baumannii 20 1082 1 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 13  854 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 22 1162 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 27 1230 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 31 1367 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 37 1459 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 55 1700 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 64 1777 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 73 1861 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 74 1877 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 86 1972 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  3  684 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  6  720 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  7  726 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 19 1079 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 21 1123 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 23 1188 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 33 1417 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 34 1431 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 38 1496 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 40 1523 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 42 1640 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 50 1666 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 51 1668 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 52 1695 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 65 1781 11 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 44 1649 12 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii   49A   1658.1 12 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii   49B   1658.2 12 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 56 1707 12 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 80 1893 12 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  5  693 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  8  749 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 10  839 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 14  865 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 16  888 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 29 1326 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 35 1440 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 41 1524 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 46 1652 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 47 1653 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 48 1657 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 57 1709 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 61 1727 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 63 1762 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 67 1806 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 75 1881 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 77 1886 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  1  649 46 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii  2  653 46 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 39 1497 16 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 24 1198 15 A33G26C28T34 A29G29C23T33 A16G14C14T16 A. baumannii 28 1243 15 A33G26C28T34 A29G29C23T33 A16G14C14T16 A. baumannii 43 1648 15 A33G26C28T34 A29G29C23T33 A16G14C14T16 A. baumannii 62 1746 15 A33G26C28T34 A29G29C23T33 A16G14C14T16 A. baumannii  4  689 15 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 68 1822 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 69   1823A 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 70   1823B 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 71 1826 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 72 1860 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 81 1924 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 82 1929 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 85 1966 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 11  841 3 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 32 1415 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 45 1651 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 54 1697 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 58 1712 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 60 1725 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 66 1802 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 76 1883 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 78 1891 24 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 79 1892 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 83 1947 24 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 84 1964 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 53 1696 24 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 36 1458 49 A34G26C29T32 A30G28C24T32 A16G14C15T15 A. baumannii 59 1716 9 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii  9  805 30 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 18  967 39 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 30 1322 48 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 26 1218 50 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. sp. 13TU 15  875 A1 A32G26C28T35 A28G28C24T34 A16G14C15T15 A. sp. 13TU 17  895 A1 A32G26C28T35 A28G28C24T34 A16G14C15T15 A. sp. 3 12  853 B7 A29G26C27T39 A26G32C21T35 A16G14C15T15 A. johnsonii 25 1202 NEW1 A32G28C26T35 A29G29C22T34 A16G14C15T15 A. sp. 2082 87 2082 NEW2 A33G27C26T35 A31G28C20T35 A16G14C15T15

TABLE 16A Base Compositions Determined from A. baumannii DNA Samples Obtained from Northwestern Medical Center and Amplified with Codon Analysis Primer Pairs Targeting the gyrA Gene PP No: 2852 PP No: 2853 PP No: 2854 Species Ibis# Isolate ST gyrA gyrA gyrA A. baumannii 54 536 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 87 665 3 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 8 80 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 9 91 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 10 92 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 11 131 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 12 137 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 21 218 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 26 242 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 94 678 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 1 9 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 2 13 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 3 19 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 4 24 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 5 36 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 6 39 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 13 139 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 15 165 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 16 170 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 17 186 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 20 202 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 22 221 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 24 234 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 25 239 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 33 370 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 34 389 10 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 19 201 14 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 27 257 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 29 301 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 31 354 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 36 422 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 37 424 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 38 434 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 39 473 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 40 482 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 44 512 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 45 516 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 47 522 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 48 526 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 50 528 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 52 531 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 53 533 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 56 542 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 59 550 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 62 556 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 64 557 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 70 588 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 73 603 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 74 605 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 75 606 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 77 611 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 79 622 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 83 643 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 85 653 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 89 669 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 93 674 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 23 228 51 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 32 369 52 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 35 393 52 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 30 339 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 41 485 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 42 493 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 43 502 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 46 520 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 49 527 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 51 529 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 65 562 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 68 579 53 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 57 546 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 58 548 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 60 552 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 61 555 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 63 557 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 66 570 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 67 578 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 69 584 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 71 593 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 72 602 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 76 609 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 78 621 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 80 625 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 81 628 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 82 632 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 84 649 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 86 655 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 88 668 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 90 671 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 91 672 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 92 673 54 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 18 196 55 A25G23C22T31 A29G28C21T43 A17G13C13T21 A. baumannii 55 537 27 A25G23C21T32 A29G28C21T43 A17G13C13T21 A. baumannii 28 263 27 A25G23C22T31 A29G28C22T42 A17G13C14T20 A. sp. 3 14 164 B7 A25G22C22T32 A30G29C22T40 A17G13C14T20 mixture 7 71 — ND ND A17G13C15T19

TABLE 16B Base Compositions Determined from A. baumannii DNA Samples Obtained from Northwestern Medical Center and Amplified with Codon Analysis Primer Pairs Targeting the parC Gene PP No: 2846 PP No: 2847 PP No: 2848 Species Ibis# Isolate ST parC parC parC A. baumannii 54 536 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 87 665 3 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 8 80 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 9 91 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 10 92 10 A33G26C28T34 A29G28C25T32 ND A. baumannii 11 131 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 12 137 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 21 218 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 26 242 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 94 678 10 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 1 9 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 2 13 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 3 19 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 4 24 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 5 36 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 6 39 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 13 139 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 15 165 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 16 170 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 17 186 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 20 202 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 22 221 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 24 234 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 25 239 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 33 370 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 34 389 10 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 19 201 14 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 27 257 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 29 301 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 31 354 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 36 422 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 37 424 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 38 434 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 39 473 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 40 482 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 44 512 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 45 516 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 47 522 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 48 526 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 50 528 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 52 531 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 53 533 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 56 542 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 59 550 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 62 556 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 64 557 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 70 588 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 73 603 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 74 605 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 75 606 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 77 611 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 79 622 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 83 643 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 85 653 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 89 669 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 93 674 51 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 23 228 51 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 32 369 52 A34G25C28T34 A30G27C25T32 A16G14C14T16 A. baumannii 35 393 52 A34G25C28T34 A30G27C25T32 A16G14C14T16 A. baumannii 30 339 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 41 485 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 42 493 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 43 502 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 46 520 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 49 527 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 51 529 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 65 562 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 68 579 53 A34G25C29T33 A30G27C26T31 A16G14C15T15 A. baumannii 57 546 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 58 548 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 60 552 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 61 555 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 63 557 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 66 570 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 67 578 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 69 584 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 71 593 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 72 602 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 76 609 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 78 621 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 80 625 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 81 628 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 82 632 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 84 649 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 86 655 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 88 668 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 90 671 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 91 672 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 92 673 54 A33G26C28T34 A29G28C25T32 A16G14C14T16 A. baumannii 18 196 55 A33G27C28T33 A29G28C25T31 A15G14C15T16 A. baumannii 55 537 27 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. baumannii 28 263 27 A33G26C29T33 A29G28C26T31 A16G14C15T15 A. sp. 3 14 164 B7 A35G25C29T32 A30G28C17T39 A16G14C15T15 mixture 7 71 — ND ND A17G14C15T14

TABLE 17A Base Compositions Determined from A. baumannii DNA Samples Obtained from Walter Reed Hospital and Amplified with Speciating Primer Pair No. 2922 and Triangulation Genotyping Analysis Primer Pair Nos. 1151 and 1156 PP No: 2922 PP No: 1151 PP No: 1156 Species Ibis# Isolate ST efp trpE Adk A. baumannii 20 1082 1 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 13  854 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 22 1162 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 27 1230 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 31 1367 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 37 1459 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 55 1700 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 64 1777 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 73 1861 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 74 1877 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 86 1972 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii  3  684 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii  6  720 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii  7  726 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 19 1079 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 21 1123 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 23 1188 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 33 1417 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 34 1431 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 38 1496 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 40 1523 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 42 1640 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 50 1666 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 51 1668 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 52 1695 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 65 1781 11 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 44 1649 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii   49A   1658.1 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii   49B   1658.2 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 56 1707 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 80 1893 12 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii  5  693 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii  8  749 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 10  839 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 14  865 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 16  888 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 29 1326 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 35 1440 14 A44G35C25T43 ND A44G32C27T37 A. baumannii 41 1524 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 46 1652 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 47 1653 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 48 1657 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 57 1709 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 61 1727 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 63 1762 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 67 1806 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 75 1881 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 77 1886 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii  1  649 46 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii  2  653 46 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 39 1497 16 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 24 1198 15 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 28 1243 15 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 43 1648 15 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 62 1746 15 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii  4  689 15 A44G35C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 68 1822 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 69   1823A 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 70   1823B 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 71 1826 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 72 1860 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 81 1924 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 82 1929 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 85 1966 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 11  841 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 32 1415 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 45 1651 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 54 1697 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 58 1712 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 60 1725 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 66 1802 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 76 1883 24 ND A43G36C20T43 A44G32C27T37 A. baumannii 78 1891 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 79 1892 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 83 1947 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 84 1964 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 53 1696 24 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 36 1458 49 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 59 1716 9 A44G35C25T43 A44G35C21T42 A44G32C26T38 A. baumannii  9  805 30 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 18  967 39 A45G34C25T43 A44G35C22T41 A44G32C26T38 A. baumannii 30 1322 48 A44G35C25T43 A43G36C20T43 A44G32C27T37 A. baumannii 26 1218 50 A44G35C25T43 A44G35C21T42 A44G32C26T38 A. sp. 13TU 15  875 A1 A47G33C24T43 A46G32C20T44 A44G33C27T36 A. sp. 13TU 17  895 A1 A47G33C24T43 A46G32C20T44 A44G33C27T36 A. sp. 3 12  853 B7 A46G35C24T42 A42G34C20T46 A43G33C24T40 A. johnsonii 25 1202 NEW1 A46G35C23T43 A42G35C21T44 A43G33C23T41 A. sp. 2082 87 2082 NEW2 A46G36C22T43 A42G32C20T48 A42G34C23T41

TABLE 17B Base Compositions Determined from A. baumannii DNA Samples Obtained from Walter Reed Hospital and Amplified with Triangulation Genotyping Analysis Primer Pair Nos. 1158 and 1160 and 1165 PP No: 1158 PP No: 1160 PP No: 1165 Species Ibis# Isolate ST mutY mutY fumC A. baumannii 20 1082 1 A27G21C25T22 A32G35C29T33 A40G33C30T36 A. baumannii 13  854 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 22 1162 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 27 1230 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 31 1367 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 37 1459 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 55 1700 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 64 1777 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 73 1861 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 74 1877 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 86 1972 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii  3  684 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii  6  720 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii  7  726 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 19 1079 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 21 1123 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 23 1188 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 33 1417 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 34 1431 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 38 1496 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 40 1523 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 42 1640 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 50 1666 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 51 1668 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 52 1695 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 65 1781 11 A27G21C25T22 A32G34C28T35 A40G33C30T36 A. baumannii 44 1649 12 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii   49A   1658.1 12 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii   49B   1658.2 12 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 56 1707 12 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 80 1893 12 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii  5  693 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii  8  749 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 10  839 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 14  865 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 16  888 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 29 1326 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 35 1440 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 41 1524 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 46 1652 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 47 1653 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 48 1657 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 57 1709 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 61 1727 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 63 1762 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 67 1806 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 75 1881 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 77 1886 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii  1  649 46 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii  2  653 46 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii 39 1497 16 A29G19C26T21 A31G35C29T34 A40G34C29T36 A. baumannii 24 1198 15 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii 28 1243 15 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii 43 1648 15 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii 62 1746 15 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii  4  689 15 A29G19C26T21 A31G35C29T34 A40G33C29T37 A. baumannii 68 1822 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 69   1823A 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 70   1823B 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 71 1826 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 72 1860 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 81 1924 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 82 1929 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 85 1966 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 11  841 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 32 1415 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 45 1651 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 54 1697 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 58 1712 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 60 1725 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 66 1802 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 76 1883 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 78 1891 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 79 1892 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 83 1947 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 84 1964 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 53 1696 24 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 36 1458 49 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 59 1716 9 A27G21C25T22 A32G35C28T34 A39G33C30T37 A. baumannii  9  805 30 A27G21C25T22 A32G35C28T34 A39G33C30T37 A. baumannii 18  967 39 A27G21C26T21 A32G35C28T34 A39G33C30T37 A. baumannii 30 1322 48 A28G21C24T22 A32G35C29T33 A40G33C30T36 A. baumannii 26 1218 50 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. sp. 13TU 15  875 A1 A27G21C25T22 A30G36C26T37 A41G34C28T36 A. sp. 13TU 17  895 A1 A27G21C25T22 A30G36C26T37 A41G34C28T36 A. sp. 3 12  853 B7 A26G23C23T23 A30G36C27T36 A39G37C26T37 A. johnsonii 25 1202 NEW1 A25G23C24T23 A30G35C30T34 A38G37C26T38 A. sp. 2082 87 2082 NEW2 A26G22C24T23 A31G35C28T35 A42G34C27T36

TABLE 17C Base Compositions Determined from A. baumannii DNA Samples Obtained from Walter Reed Hospital and Amplified with Triangulation Genotyping Analysis Primer Pair Nos. 1167 and 1170 and 1171 PP No: 1167 PP No: 1170 PP No: 1171 Species Ibis# Isolate ST fumC fumC ppa A. baumannii 20 1082 1 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 13  854 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 22 1162 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 27 1230 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 31 1367 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 37 1459 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 55 1700 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 64 1777 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 73 1861 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 74 1877 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 86 1972 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii  3  684 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii  6  720 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii  7  726 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 19 1079 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 21 1123 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 23 1188 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 33 1417 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 34 1431 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 38 1496 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 40 1523 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 42 1640 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 50 1666 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 51 1668 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 52 1695 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 65 1781 11 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 44 1649 12 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii   49A   1658.1 12 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii   49B   1658.2 12 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 56 1707 12 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 80 1893 12 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii  5  693 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii  8  749 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 10  839 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 14  865 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 16  888 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 29 1326 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 35 1440 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 41 1524 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 46 1652 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 47 1653 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 48 1657 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 57 1709 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 61 1727 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 63 1762 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 67 1806 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 75 1881 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 77 1886 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii  1  649 46 A41G35C32T39 A37G28C20T51 A35G37C32T45 A. baumannii  2  653 46 A41G35C32T39 A37G28C20T51 A35G37C32T45 A. baumannii 39 1497 16 A41G35C32T39 A37G28C20T51 A35G37C30T47 A. baumannii 24 1198 15 A41G35C32T39 A37G28C20T51 A35G37C30T47 A. baumannii 28 1243 15 A41G35C32T39 A37G28C20T51 A35G37C30T47 A. baumannii 43 1648 15 A41G35C32T39 A37G28C20T51 A35G37C30T47 A. baumannii 62 1746 15 A41G35C32T39 A37G28C20T51 A35G37C30T47 A. baumannii  4  689 15 A41G35C32T39 A37G28C20T51 A35G37C30T47 A. baumannii 68 1822 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 69   1823A 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 70   1823B 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 71 1826 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 72 1860 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 81 1924 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 82 1929 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 85 1966 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 11  841 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 32 1415 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 45 1651 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 54 1697 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 58 1712 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 60 1725 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 66 1802 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 76 1883 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 78 1891 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 79 1892 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 83 1947 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 84 1964 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 53 1696 24 A40G35C34T38 A39G26C22T49 A35G37C33T44 A. baumannii 36 1458 49 A40G35C34T38 A39G26C22T49 A35G37C30T47 A. baumannii 59 1716 9 A40G35C32T40 A38G27C20T51 A36G35C31T47 A. baumannii  9  805 30 A40G35C32T40 A38G27C21T50 A35G36C29T49 A. baumannii 18  967 39 A40G35C33T39 A38G27C20T51 A35G37C30T47 A. baumannii 30 1322 48 A40G35C35T37 A38G27C21T50 A35G37C30T47 A. baumannii 26 1218 50 A40G35C34T38 A38G27C21T50 A35G37C33T44 A. sp. 13TU 15  875 A1 A41G39C31T36 A37G26C24T49 A34G38C31T46 A. sp. 13TU 17  895 A1 A41G39C31T36 A37G26C24T49 A34G38C31T46 A. sp. 3 12  853 B7 A43G37C30T37 A36G27C24T49 A34G37C31T47 A. johnsonii 25 1202 NEW1 A42G38C31T36 A40G27C19T50 A35G37C32T45 A. sp. 2082 87 2082 NEW2 A43G37C32T35 A37G26C21T52 A35G38C31T45

TABLE 18A Base Compositions Determined from A. baumannii DNA Samples Obtained from Northwestern Medical Center and Amplified with Speciating Primer Pair No. 2922 and Triangulation Genotyping Analysis Primer Pair Nos. 1151 and 1156 PP No: 2922 PP No: 1151 PP No: 1156 Species Ibis# Isolate ST efp trpE adk A. baumannii 54 536 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 87 665 3 A44G35C24T44 A44G35C22T41 A44G32C26T38 A. baumannii 8 80 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 9 91 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 10 92 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 11 131 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 12 137 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 21 218 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 26 242 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 94 678 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 1 9 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 2 13 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 3 19 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 4 24 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 5 36 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 6 39 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 13 139 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 15 165 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 16 170 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 17 186 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 20 202 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 22 221 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 24 234 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 25 239 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 33 370 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 34 389 10 A45G34C25T43 A44G35C21T42 A44G32C26T38 A. baumannii 19 201 14 A44G35C25T43 A44G35C22T41 A44G32C27T37 A. baumannii 27 257 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 29 301 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 31 354 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 36 422 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 37 424 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 38 434 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 39 473 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 40 482 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 44 512 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 45 516 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 47 522 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 48 526 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 50 528 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 52 531 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 53 533 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 56 542 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 59 550 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 62 556 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 64 557 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 70 588 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 73 603 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 74 605 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 75 606 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 77 611 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 79 622 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 83 643 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 85 653 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 89 669 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 93 674 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 23 228 51 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 32 369 52 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 35 393 52 A44G35C25T43 A43G36C20T43 A44G32C26T38 A. baumannii 30 339 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 41 485 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 42 493 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 43 502 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 46 520 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 49 527 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 51 529 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 65 562 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 68 579 53 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 57 546 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 58 548 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 60 552 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 61 555 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 63 557 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 66 570 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 67 578 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 69 584 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 71 593 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 72 602 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 76 609 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 78 621 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 80 625 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 81 628 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 82 632 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 84 649 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 86 655 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 88 668 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 90 671 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 91 672 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 92 673 54 A44G35C25T43 A44G35C20T43 A44G32C26T38 A. baumannii 18 196 55 A44G35C25T43 A44G35C20T43 A44G32C27T37 A. baumannii 55 537 27 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. baumannii 28 263 27 A44G35C25T43 A44G35C19T44 A44G32C27T37 A. sp. 3 14 164 B7 A46G35C24T42 A42G34C20T46 A43G33C24T40 mixture 7 71 ? mixture ND ND

TABLE 18B Base Compositions Determined from A. baumannii DNA Samples Obtained from Northwestern Medical Center and Amplified with Triangulation Genotyping Analysis Primer Pair Nos. 1158, 1160 and 1165 PP No: 1158 PP No: 1160 PP No: 1165 Species Ibis# Isolate ST mutY mutY fumC A. baumannii 54 536 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 87 665 3 A27G20C27T21 A32G35C28T34 A40G33C30T36 A. baumannii 8 80 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 9 91 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 10 92 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 11 131 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 12 137 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 21 218 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 26 242 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 94 678 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 1 9 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 2 13 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 3 19 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 4 24 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 5 36 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 6 39 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 13 139 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 15 165 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 16 170 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 17 186 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 20 202 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 22 221 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 24 234 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 25 239 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 33 370 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 34 389 10 A27G21C26T21 A32G35C28T34 A40G33C30T36 A. baumannii 19 201 14 A27G21C25T22 A31G36C28T34 A40G33C29T37 A. baumannii 27 257 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 29 301 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 31 354 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 36 422 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 37 424 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 38 434 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 39 473 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 40 482 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 44 512 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 45 516 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 47 522 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 48 526 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 50 528 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 52 531 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 53 533 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 56 542 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 59 550 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 62 556 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 64 557 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 70 588 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 73 603 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 74 605 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 75 606 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 77 611 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 79 622 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 83 643 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 85 653 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 89 669 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 93 674 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 23 228 51 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 32 369 52 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 35 393 52 A27G21C25T22 A32G35C28T34 A40G33C29T37 A. baumannii 30 339 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 41 485 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 42 493 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 43 502 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 46 520 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 49 527 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 51 529 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 65 562 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 68 579 53 A28G20C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 57 546 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 58 548 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 60 552 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 61 555 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 63 557 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 66 570 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 67 578 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 69 584 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 71 593 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 72 602 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 76 609 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 78 621 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 80 625 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 81 628 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 82 632 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 84 649 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 86 655 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 88 668 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 90 671 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 91 672 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 92 673 54 A27G21C26T21 A32G34C29T34 A40G33C30T36 A. baumannii 18 196 55 A27G21C25T22 A31G36C27T35 A40G33C29T37 A. baumannii 55 537 27 A27G21C25T22 A32G35C28T34 A40G33C30T36 A. baumannii 28 263 27 A27G21C25T22 A32G35C28T34 A40G33C30T36 A. sp. 3 14 164 B7 A26G23C23T23 A30G36C27T36 A39G37C26T37 mixture 7 71 ? ND ND ND

TABLE 18C Base Compositions Determined from A. baumannii DNA Samples Obtained from Northwestern Medical Center and Amplified with Triangulation Genotyping Analysis Primer Pair Nos. 1167, 1170 and 1171 PP No: 1167 PP No: 1170 PP No: 1171 Species Ibis# Isolate ST fumC fumC ppa A. baumannii 54 536 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 87 665 3 A41G34C35T37 A38G27C20T51 A35G37C31T46 A. baumannii 8 80 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 9 91 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 10 92 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 11 131 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 12 137 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 21 218 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 26 242 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 94 678 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 1 9 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 2 13 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 3 19 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 4 24 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 5 36 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 6 39 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 13 139 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 15 165 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 16 170 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 17 186 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 20 202 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 22 221 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 24 234 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 25 239 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 33 370 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 34 389 10 A41G34C34T38 A38G27C21T50 A35G37C33T44 A. baumannii 19 201 14 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 27 257 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 29 301 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 31 354 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 36 422 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 37 424 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 38 434 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 39 473 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 40 482 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 44 512 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 45 516 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 47 522 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 48 526 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 50 528 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 52 531 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 53 533 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 56 542 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 59 550 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 62 556 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 64 557 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 70 588 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 73 603 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 74 605 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 75 606 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 77 611 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 79 622 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 83 643 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 85 653 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 89 669 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 93 674 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 23 228 51 A40G35C34T38 A38G27C21T50 A35G37C30T47 A. baumannii 32 369 52 A40G35C34T38 A38G27C21T50 A35G37C31T46 A. baumannii 35 393 52 A40G35C34T38 A38G27C21T50 A35G37C31T46 A. baumannii 30 339 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 41 485 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 42 493 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 43 502 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 46 520 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 49 527 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 51 529 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 65 562 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 68 579 53 A40G35C35T37 A38G27C21T50 A35G37C31T46 A. baumannii 57 546 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 58 548 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 60 552 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 61 555 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 63 557 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 66 570 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 67 578 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 69 584 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 71 593 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 72 602 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 76 609 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 78 621 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 80 625 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 81 628 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 82 632 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 84 649 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 86 655 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 88 668 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 90 671 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 91 672 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 92 673 54 A40G35C34T38 A39G26C22T49 A35G37C31T46 A. baumannii 18 196 55 A42G34C33T38 A38G27C20T51 A35G37C31T46 A. baumannii 55 537 27 A40G35C33T39 A38G27C20T51 A35G37C33T44 A. baumannii 28 263 27 A40G35C33T39 A38G27C20T51 A35G37C33T44 A. sp. 3 14 164 B7 A43G37C30T37 A36G27C24T49 A34G37C31T47 mixture 7 71 — ND ND ND

Base composition analysis of the samples obtained from Walter Reed hospital indicated that a majority of the strain types identified were the same strain types already characterized by the OIF study of Example 12. This is not surprising since at least some patients from which clinical samples were obtained in OIF were transferred to the Walter Reed Hospital (WRAIR). Examples of these common strain types include: ST10, ST11, ST12, ST14, ST15, ST16 and ST46. A strong correlation was noted between these strain types and the presence of mutations in the gyrA and parC which confer quinolone drug resistance.

In contrast, the results of base composition analysis of samples obtained from Northwestern Medical Center indicate the presence of 4 major strain types: ST10, ST51, ST53 and ST54. All of these strain types have the gyrA quinolone resistance mutation and most also have the parC quinolone resistance mutation, with the exception of ST35. This observation is consistent with the current understanding that the gyrA mutation generally appears before the parC mutation and suggests that the acquisition of these drug resistance mutations is rather recent and that resistant isolates are taking over the wild-type isolates. Another interesting observation was that a single isolate of ST3 (isolate 841) displays a triangulation genotyping analysis pattern similar to other isolates of ST3, but the codon analysis amplification product base compositions indicate that this isolate has not yet undergone the quinolone resistance mutations in gyrA and parC.

The six isolates that represent species other than Acinetobacter baumannii in the samples obtained from the Walter Reed Hospital were each found to not carry the drug resistance mutations.

The results described above involved analysis of 183 samples using the methods and compositions of the present invention. Results were provided to collaborators at the Walter Reed hospital and Northwestern Medical center within a week of obtaining samples. This example highlights the rapid throughput characteristics of the analysis platform and the resolving power of triangulation genotyping analysis and codon analysis for identification of and determination of drug resistance in bacteria.

Example 14 Identification of Drug Resistance Genes and Virulence Factors in Staphylococcus aureus

An eight primer pair panel was designed for identification of drug resistance genes and virulence factors of Staphylococcus aureus and is shown in Table 19. The primer sequences are found in Table 2 and are cross-referenced by the primer pair numbers, primer pair names or SEQ ID NOs listed in Table 19. TABLE 19 Primer Pairs for Identification of Drug Resistance Genes and Virulence Factors in Staphylococcus aureus Forward Reverse Primer Primer Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name NO:) Reverse Primer Name NO:) Gene 879 MECA_Y14051_4507_4530_F 288 MECA_Y14051_4555_4581_R 1269 mecA 2056 MECI-R_NC003923-41798- 698 MECI-R_NC003923-41798- 1420 MecI-R 41609_33_60_F 41609_86_113_R 2081 ERMA_NC002952-55890- 217 ERMA_NC002952-55890- 1167 ermA 56621_366_395_F 56621_438_465_R 2086 ERMC_NC005908-2004- 399 ERMC_NC005908-2004- 1041 ermC 2738_85_116_F 2738_173_206_R 2095 PVLUK_NC003923-1529595- 456 PVLUK_NC003923-1529595- 1261 Pv-luk 1531285_688_713_F 1531285_775_804_R 2249 TUFB_NC002758-615038- 430 TUFB_NC002758-615038- 1321 tufB 616222_696_725_F 616222_793_820_R 2256 NUC_NC002758-894288- 174 NUC_NC002758-894288- 853 Nuc 894974_316_345_F 894974_396_421_R 2313 MUPR_X75439_2486_2516_F 172 MUPR_X75439_2548_2574_R 1360 mupR

Primer pair numbers 2256 and 2249 are confirmation primers designed with the aim of high level identification of Staphylococcus aureus. The nuc gene is a Staphylococcus aureus-specific marker gene. The tufB gene is a universal housekeeping gene but the bioagent identifying amplicon defined by primer pair number 2249 provides a unique base composition (A43 G28 C19 T35) which distinguishes Staphylococcus aureus from other members of the genus Staphylococcus.

High level methicillin resistance in a given strain of Staphylococcus aureus is indicated by bioagent identifying amplicons defined by primer pair numbers 879 and 2056. Analyses have indicated that primer pair number 879 is not expected to prime S. sciuri homolog or Enterococcus faecalis/faciem ampicillin-resistant PBP5 homologs.

Macrolide and erythromycin resistance in a given strain of Staphylococcus aureus is indicated by bioagent identifying amplicons defined by primer pair numbers 2081 and 2086.

Resistance to mupriocin in a given strain of Staphylococcus aureus is indicated by bioagent identifying amplicons defined by primer pair number 2313.

Virulence in a given strain of Staphylococcus aureus is indicated by bioagent identifying amplicons defined by primer pair number 2095. This primer pair can simultaneously and identify the pvl (lukS-PV) gene and the lukD gene which encodes a homologous enterotoxin. A bioagent identifying amplicon of the lukD gene has a six nucleobase length difference relative to the lukS-PV gene.

A total of 32 blinded samples of different strains of Staphylococcus aureus were provided by the Center for Disease Control (CDC). Each sample was analyzed by PCR amplification with the eight primer pair panel, followed by purification and measurement of molecular masses of the amplification products by mass spectrometry. Base compositions for the amplification products were calculated. The base compositions provide the information summarized above for each primer pair. The results are shown in Tables 20A and B. One result noted upon un-blinding of the samples is that each of the PVL+identifications agreed with PVL+identified in the same samples by standard PCR assays. These results indicate that the panel of eight primer pairs is useful for identification of drug resistance and virulence sub-species characteristics for Staphylococcus aureus. It is expected that a kit comprising one or more of the members of this panel will be a useful embodiment of the present invention. TABLE 20A Drug Resistance and Virulence Identified in Blinded Samples of Various Strains of Staphylococcus aureus with Primer Pair Nos. 2081, 2086, 2095 and 2256 Primer Primer Primer Sample Pair No. Pair No. Primer Pair No. Pair No. Index No. 2081 (ermA) 2086 (ermC) 2095 (pv-luk) 2256 (nuc) CDC0010 − − PVL−/lukD+ + CDC0015 − − PVL+/lukD+ + CDC0019 − + PVL−/lukD+ + CDC0026 + − PVL−/lukD+ + CDC0030 + − PVL−/lukD+ + CDC004 − − PVL+/lukD+ + CDC0014 − + PVL+/lukD+ + CDC008 − − PVL−/lukD+ + CDC001 + − PVL−/lukD+ + CDC0022 + − PVL−/lukD+ + CDC006 + − PVL−/lukD+ + CDC007 − − PVL−/lukD+ + CDCVRSA1 + − PVL−/lukD+ + CDCVRSA2 + + PVL−/lukD+ + CDC0011 + − PVL−/lukD+ + CDC0012 − − PVL+/lukD− + CDC0021 + − PVL−/lukD+ + CDC0023 + − PVL−/lukD+ + CDC0025 + − PVL−/lukD+ + CDC005 − − PVL−/lukD+ + CDC0018 + − PVL+/lukD− + CDC002 − − PVL−/lukD+ + CDC0028 + − PVL−/lukD+ + CDC003 − − PVL−/lukD+ + CDC0013 − − PVL+/lukD+ + CDC0016 − − PVL−/lukD+ + CDC0027 + − PVL−/lukD+ + CDC0029 − − PVL+/lukD+ + CDC0020 − + PVL−/lukD+ + CDC0024 − − PVL−/lukD+ + CDC0031 − − PVL−/lukD+ +

TABLE 20B Drug Resistance and Virulence Identified in Blinded Samples of Various Strains of Staphylococcus aureus with Primer Pair Nos. 2249, 879, 2056, and 2313 Primer Primer Primer Pair No. Pair No. Pair No. Sample Primer Pair No. 2249 879 2056 2313 Index No. (tufB) (mecA) (mecI-R) (mupR) CDC0010 Staphylococcus aureus + + − CDC0015 Staphylococcus aureus − − − CDC0019 Staphylococcus aureus + + − CDC0026 Staphylococcus aureus + + − CDC0030 Staphylococcus aureus + + − CDC004 Staphylococcus aureus + + − CDC0014 Staphylococcus aureus + + − CDC008 Staphylococcus aureus + + − CDC001 Staphylococcus aureus + + − CDC0022 Staphylococcus aureus + + − CDC006 Staphylococcus aureus + + + CDC007 Staphylococcus aureus + + − CDCVRSA1 Staphylococcus aureus + + − CDCVRSA2 Staphylococcus aureus + + − CDC0011 Staphylococcus aureus − − − CDC0012 Staphylococcus aureus + + − CDC0021 Staphylococcus aureus + + − CDC0023 Staphylococcus aureus + + − CDC0025 Staphylococcus aureus + + − CDC005 Staphylococcus aureus + + − CDC0018 Staphylococcus aureus + + − CDC002 Staphylococcus aureus + + − CDC0028 Staphylococcus aureus + + − CDC003 Staphylococcus aureus + + − CDC0013 Staphylococcus aureus + + − CDC0016 Staphylococcus aureus + + − CDC0027 Staphylococcus aureus + + − CDC0029 Staphylococcus aureus + + − CDC0020 Staphylococcus aureus − − − CDC0024 Staphylococcus aureus + + − CDC0031 Staphylococcus scleiferi − − −

Example 15 Selection and Use of Triangulation Genotyping Analysis Primer Pairs for Staphylococcus aureus

To combine the power of high-throughput mass spectrometric analysis of bioagent identifying amplicons with the sub-species characteristic resolving power provided by triangulation genotyping analysis, a panel of eight triangulation genotyping analysis primer pairs was selected. The primer pairs are designed to produce bioagent identifying amplicons within six different housekeeping genes which are listed in Table 21. The primer sequences are found in Table 2 and are cross-referenced by the primer pair numbers, primer pair names or SEQ ID NOs listed in Table 21. TABLE 21 Primer Pairs for Triangulation Genotyping Analysis of Staphylococcus aureus Forward Reverse Primer Primer Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name NO:) Reverse Primer Name NO:) Gene 2146 ARCC_NC003923-2725050- 437 ARCC_NC003923-2725050- 1137 arcC 2724595_131_161_F 2724595_214_245_R 2149 AROE_NC003923-1674726- 530 AROE_NC003923-1674726- 891 aroE 1674277_30_62_F 1674277_155_181_R 2150 AROE_NC003923-1674726- 474 AROE_NC003923-1674726- 869 aroE 1674277_204_232_F 1674277_308_335_R 2156 GMK_NC003923-1190906- 268 GMK_NC003923-1190906- 1284 gmk 1191334_301_329_F 1191334_403_432_R 2157 PTA_NC003923-628885- 418 PTA_NC003923-628885- 1301 pta 629355_237_263_F 629355_314_345_R 2161 TPI_NC003923-830671- 318 TPI_NC003923-830671- 1300 tpi 831072_1_34_F 831072_97_129_R 2163 YQI_NC003923-378916- 440 YQI_NC003923-378916- 1076 yqi 379431_142_167_F 379431_259_284_R 2166 YQI_NC003923-378916- 219 YQI_NC003923-378916- 1013 yqi 379431_275_300_F 379431_364_396_R

The same samples analyzed for drug resistance and virulence in Example 14 were subjected to triangulation genotyping analysis. The primer pairs of Table 21 were used to produce amplification products by PCR, which were subsequently purified and measured by mass spectrometry. Base compositions were calculated from the molecular masses and are shown in Tables 22A and 22B. TABLE 22A Triangulation Genotyping Analysis of Blinded Samples of Various Strains of Staphylococcus aureus with Primer Pair Nos. 2146, 2149, 2150 and 2156 Sample Primer Pair No. Primer Pair No. Primer Pair No. Primer Pair No. Index No. Strain 2146 (arcC) 2149(aroE) 2150 (aroE) 2156 (gmk) CDC0010 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0015 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0019 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0026 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0030 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC004 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0014 COL A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC008 ???? A44 G24 C18 T29 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC001 Mu50 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31 CDC0022 Mu50 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31 CDC006 Mu50 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31 CDC0011 MRSA252 A45 G24 C18 T28 A58 G24 C19 T51 A41 G36 C12 T43 A51 G29 C21 T31 CDC0012 MRSA252 A45 G24 C18 T28 A58 G24 C19 T51 A41 G36 C12 T43 A51 G29 C21 T31 CDC0021 MRSA252 A45 G24 C18 T28 A58 G24 C19 T51 A41 G36 C12 T43 A51 G29 C21 T31 CDC0023 ST:110 A45 G24 C18 T28 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0025 ST:110 A45 G24 C18 T28 A59 G24 C18 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC005 ST:338 A44 G24 C18 T29 A59 G23 C19 T51 A40 G36 C14 T42 A51 G29 C21 T31 CDC0018 ST:338 A44 G24 C18 T29 A59 G23 C19 T51 A40 G36 C14 T42 A51 G29 C21 T31 CDC002 ST:108 A46 G23 C20 T26 A58 G24 C19 T51 A42 G36 C12 T42 A51 G29 C20 T32 CDC0028 ST:108 A46 G23 C20 T26 A58 G24 C19 T51 A42 G36 C12 T42 A51 G29 C20 T32 CDC003 ST:107 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31 CDC0013 ST:12 ND A59 G24 C18 T51 A40 G36 C13 T43 A51 G29 C21 T31 CDC0016 ST:120 A45 G23 C18 T29 A58 G24 C19 T51 A40 G37 C13 T42 A51 G29 C21 T31 CDC0027 ST:105 A45 G23 C20 T27 A58 G24 C18 T52 A40 G36 C13 T43 A51 G29 C21 T31 CDC0029 MSSA476 A45 G23 C20 T27 A58 G24 C19 T51 A40 G36 C13 T43 A50 G30 C20 T32 CDC0020 ST:15 A44 G23 C21 T27 A59 G23 C18 T52 A40 G36 C13 T43 A50 G30 C20 T32 CDC0024 ST:137 A45 G23 C20 T27 A57 G25 C19 T51 A40 G36 C13 T43 A51 G29 C22 T30 CDC0031 *** No product No product No product No product

TABLE 22B Triangulation Genotyping Analysis of Blinded Samples of Various Strains of Staphylococcus aureus with Primer Pair Nos. 2146, 2149, 2150 and 2156 Sample Primer Pair No. Primer Pair No. Primer Pair No. Primer Pair No. Index No. Strain 2157 (pta) 2161 (tpi) 2163 (yqi) 2166 (yqi) CDC0010 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0015 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0019 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0026 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0030 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC004 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0014 COL A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC008 unknown A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC001 Mu50 A33 G25 C22 T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36 CDC0022 Mu50 A33 G25 C22 T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36 CDC006 Mu50 A33 G25 C22 T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36 CDC0011 MRSA252 A32 G25 C23 T29 A50 G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC0012 MRSA252 A32 G25 C23 T29 A50 G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC0021 MRSA252 A32 G25 C23 T29 A50 G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC0023 ST:110 A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0025 ST:110 A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC005 ST:338 A32 G25 C24 T28 A51 G27 C21 T30 A42 G36 C22 T43 A37 G30 C18 T37 CDC0018 ST:338 A32 G25 C24 T28 A51 G27 C21 T30 A42 G36 C22 T43 A37 G30 C18 T37 CDC002 ST:108 A33 G25 C23 T28 A50 G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC0028 ST:108 A33 G25 C23 T28 A50 G28 C22 T29 A42 G36 C22 T43 A37 G30 C18 T37 CDC003 ST:107 A32 G25 C23 T29 A51 G28 C22 T28 A41 G37 C22 T43 A37 G30 C18 T37 CDC0013 ST:12 A32 G25 C23 T29 A51 G28 C22 T28 A42 G36 C22 T43 A37 G30 C18 T37 CDC0016 ST:120 A32 G25 C24 T28 A50 G28 C21 T30 A42 G36 C22 T43 A37 G30 C18 T37 CDC0027 ST:105 A33 G25 C22 T29 A50 G28 C22 T29 A43 G36 C21 T43 A36 G31 C19 T36 CDC0029 MSSA476 A33 G25 C22 T29 A50 G28 C22 T29 A42 G36 C22 T43 A36 G31 C19 T36 CDC0020 ST:15 A33 G25 C22 T29 A50 G28 C21 T30 A42 G36 C22 T43 A36 G31 C18 T37 CDC0024 ST:137 A33 G25 C22 T29 A51 G28 C22 T28 A42 G36 C22 T43 A37 G30 C18 T37 CDC0031 *** A34 G25 C25 T25 A51 G27 C24 T27 No product No product Note: *** The sample CDC0031 was identified as Staphylococcus scleiferi as indicated in Example 14. Thus, the triangulation genotyping primers designed for Staphylococcus aureus would generally not be expected to prime and produce amplification products of this organism. Tables 22A and 22B indicate that amplification products are obtained for this organism only with primer pair numbers 2157 and 2161.

A total of thirteen different genotypes of Staphylococcus aureus were identified according to the unique combinations of base compositions across the eight different bioagent identifying amplicons obtained with the eight primer pairs. These results indicate that this eight primer pair panel is useful for analysis of unknown or newly emerging strains of Staphylococcus aureus. It is expected that a kit comprising one or more of the members of this panel will be a useful embodiment of the present invention.

Example 16 Selection and Use of Triangulation Genotyping Analysis Primer Pairs for Members of the Bacterial Genus Vibrio

To combine the power of high-throughput mass spectrometric analysis of bioagent identifying amplicons with the sub-species characteristic resolving power provided by triangulation genotyping analysis, a panel of eight triangulation genotyping analysis primer pairs was selected. The primer pairs are designed to produce bioagent identifying amplicons within seven different housekeeping genes which are listed in Table 23. The primer sequences are found in Table 2 and are cross-referenced by the primer pair numbers, primer pair names or SEQ ID NOs listed in Table 23. TABLE 23 Primer Pairs for Triangulation Genotyping Analysis of Members of the Bacterial Genus Vibrio Forward Reverse Primer Primer Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name NO:) Reverse Primer Name NO:) Gene 1098 RNASEP_VBC_331_349_F 325 RNASEP_VBC_388_414_R 1163 RNAse P 2000 CTXB_NC002505_46_70_F 278 CTXB_NC002505_132_162_R 1039 ctxB 2001 FUR_NC002505_87_113_F 465 FUR_NC002505_205_228_R 1037 fur 2011 GYRB_NC002505_1161_1190_F 148 GYRB_NC002505_1255_1284_R 1172 gyrB 2012 OMPU_NC002505_85_110_F 190 OMPU_NC002505_154_180_R 1254 ompU 2014 OMPU_NC002505_431_455_F 266 OMPU_NC002505_544_567_R 1094 ompU 2323 CTXA_NC002505-1568114- 508 CTXA_NC002505-1568114- 1297 ctxA 1567341_122_149_F 1567341_186_214_R 2927 GAPA_NC002505_694_721_F 259 GAPA_NC_002505_29_58_R 1060 gapA

A group of 50 bacterial isolates containing multiple strains of both environmental and clinical isolates of Vibrio cholerae, 9 other Vibrio species, and 3 species of Photobacteria were tested using this panel of primer pairs. Base compositions of amplification products obtained with these 8 primer pairs were used to distinguish amongst various species tested, including sub-species differentiation within Vibrio cholerae isolates. For instance, the non-O1/non-O1 39 isolates were clearly resolved from the O1 and the O139 isolates, as were several of the environmental isolates of Vibrio cholerae from the clinical isolates.

It is expected that a kit comprising one or more of the members of this panel will be a useful embodiment of the present invention.

Example 17 Selection and Use of Triangulation Genotyping Analysis Primer Pairs for Members of the Bacterial Genus Pseudomonas

To combine the power of high-throughput mass spectrometric analysis of bioagent identifying amplicons with the sub-species characteristic resolving power provided by triangulation genotyping analysis, a panel of twelve triangulation genotyping analysis primer pairs was selected. The primer pairs are designed to produce bioagent identifying amplicons within seven different housekeeping genes which are listed in Table 24. The primer sequences are found in Table 2 and are cross-referenced by the primer pair numbers, primer pair names or SEQ ID NOs listed in Table 24. TABLE 24 Primer Pairs for Triangulation Genotyping Analysis of Members of the Bacterial Genus Pseudomonas Forward Reverse Primer Primer Primer Pair (SEQ ID (SEQ ID Target No. Forward Primer Name NO:) Reverse Primer Name NO:) Gene 2949 ACS_NC002516-970624- 376 ACS_NC002516-970624- 1265 acsA 971013_299_316_F 971013_364_383_R 2950 ARO_NC002516-26883- 267 ARO_NC002516-26883- 1341 aroE 27380_4_26_F 27380_111_128_R 2951 ARO_NC002516-26883- 705 ARO_NC002516-26883- 1056 aroE 27380_356_377_F 27380_459_484_R 2954 GUA_NC002516-4226546- 710 GUA_NC002516-4226546- 1259 guaA 4226174_155_178_F 4226174_265_287_R 2956 GUA_NC002516-4226546- 374 GUA_NC002516-4226546- 1111 guaA 4226174_242_263_F 4226174_355_371_R 2957 MUT_NC002516-5551158- 545 MUT_NC002516-5551158- 978 mutL 5550717_5_26_F 5550717_99_116_R 2959 NUO_NC002516-2984589- 249 NUO_NC002516-2984589- 1095 nuoD 2984954_8_26_F 2984954_97_117_R 2960 NUO_NC002516-2984589- 195 NUO_NC002516-2984589- 1376 nuoD 2984954_218_239_F 2984954_301_326_R 2961 PPS_NC002516-1915014- 311 PPS_NC002516-1915014- 1014 pps 1915383_44_63_F 1915383_140_165_R 2962 PPS_NC002516-1915014- 365 PPS_NC002516-1915014- 1052 pps 1915383_240_258_F 1915383_341_360_R 2963 TRP_NC002516-671831- 527 TRP_NC002516-671831- 1071 trpE 672273_24_42_F 672273_131_150_R 2964 TRP_NC002516-671831- 490 TRP_NC002516-671831- 1182 trpE 672273_261_282_F 672273_362_383_R

It is expected that a kit comprising one or more of the members of this panel will be a useful embodiment of the present invention.

The present invention includes any combination of the various species and subgeneric groupings falling within the generic disclosure. This invention therefore includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.

While in accordance with the patent statutes, description of the various embodiments and examples have been provided, the scope of the invention is not to be limited thereto or thereby. Modifications and alterations of the present invention will be apparent to those skilled in the art without departing from the scope and spirit of the present invention.

Therefore, it will be appreciated that the scope of this invention is to be defined by the appended claims, rather than by the specific examples which have been presented by way of example.

Each reference (including, but not limited to, journal articles, U.S. and non-U.S. patents, patent application publications, international patent application publications, gene bank gi or accession numbers, internet web sites, and the like) cited in the present application is incorporated herein by reference in its entirety. 

1. An oligonucleotide primer pair comprising a forward and a reverse primer, each comprising between 13 and 35 linked nucleotides in length, designed to generate an amplicon that is between about 45 and about 200 linked nucleotides in length, wherein said forward primer comprises at least 80% complementarity to a first region within nucleotides 1-286 of a reference sequence, said reference sequence being a sequence extraction of coordinates 830671-831072 of Genbank gi number 21281729, and wherein said reverse primer comprises at least 80% complementarity to a second region within nucleotides 1-286 of said reference sequence.
 2. The oligonucleotide primer pair of claim 1 wherein said forward primer comprises at least 90% complementarity to said first region, and wherein said first region is within nucleotides 1-34 of said reference sequence.
 3. The oligonucleotide primer pair of claim 2 wherein said forward primer comprises at least 95% complementarity to said first region.
 4. The oligonucleotide primer pair of claim 3 wherein said forward primer comprises 100% complementarity to said first region.
 5. The oligonucleotide primer pair of claim 1 wherein said forward primer is SEQ ID NO:
 318. 6. The oligonucleotide primer pair of claim 1 wherein said reverse primer comprises at least 90% complementarity to said second region, and wherein said second region is within nucleotides 97-129 of said reference sequence.
 7. The oligonucleotide primer pair of claim 6 wherein said reverse primer comprises at least 95% complementarity to said second region.
 8. The oligonucleotide primer pair of claim 7 wherein said reverse primer comprises 100% complementarity to said second region.
 9. The oligonucleotide primer pair of claim 1 wherein said reverse primer is SEQ ID NO:
 1300. 10. The oligonucleotide primer pair of claim 1 wherein at least one of said forward primer and said reverse primer comprises at least one modified nucleobase.
 11. The oligonucleotide primer pair of claim 10 wherein at least one of said at least one modified nucleobase is a mass modified nucleobase.
 12. The oligonucleotide primer pair of claim 11 wherein said mass modified nucleobase is 5-Iodo-C.
 13. The composition of claim 11 wherein said mass modified nucleobase comprises a molecular mass modifying tag.
 14. The oligonucleotide primer pair of claim 10 wherein at least one of said at least one modified nucleobase is a universal nucleobase.
 15. The oligonucleotide primer pair of claim 14 wherein said universal nucleobase is inosine.
 16. The oligonucleotide primer pair of claim 1 wherein at least one of said forward primer and said reverse primer comprises a non-templated T residue at its 5′ end.
 17. A kit for identifying, determining one or more characteristics of, or detecting a Staphylococcus aureus bioagent comprising the oligonucleotide primer pair of claim 1 and at least one additional primer pair designed to hybridize to a Staphylococcus aureus gene encoding arcC, aroE, gmk, pta, yqi, or a combination thereof.
 18. The kit of claim 17 further comprising at least one other additional primer pair designed to hybridize to a Staphylococcus aureus gene encoding mecA, mecRI, pvluk, or a combination thereof.
 19. The kit of claim 17 wherein said at least one additional primer pair comprises SEQ ID NOs: 437:1232, SEQ ID NOs: 590:891, SEQ ID NOs: 474:869, SEQ ID NOs: 268:1284, SEQ ID NOs: 418:1301, SEQ ID NOs: 440:1076, SEQ ID NOs: 219:1013, or a combination thereof.
 20. The kit of claim 17 wherein said oligonucleotide primer pair of claim 1 and said at least one additional primer pair consists of eight oligonucleotide primer pairs having at least 70% sequence identity with the primer pairs represented by: SEQ ID NOs: 437:1232, SEQ ID NOs: 590:891, SEQ ID NOs: 474:869, SEQ ID NOs: 268:1284, SEQ ID NOs: 418:1301, SEQ ID NOs: 318:1300, SEQ ID NOs: 440:1076, and SEQ ID NOs: 219:1013.
 21. A method for identifying, determining one or more characteristics of, or detecting a Staphylococcus aureus bioagent in a sample comprising: a) amplifying a nucleic acid from said sample using an oligonucleotide primer pair targeted to a Staphylococcus aureus tpi gene comprising a forward and a reverse primer, each being between 13 and 35 linked nucleotides in length, wherein said forward primer comprises at least 70% complementarity to a first region within nucleotides 1-286 of a reference sequence, said reference sequence being a sequence extraction of coordinates 830671-831072 of Genbank gi number 21281729, and wherein said reverse primer comprises at least 70% complementarity to a second region within nucleotides 1-286 of said reference sequence, wherein said amplifying generates at least one amplification product that comprises between about 45 and about 200 linked nucleotides; and b) determining the molecular mass of said at least one amplification product by mass spectrometry.
 22. The method of claim 21 further comprising comparing said determined molecular mass to a plurality of molecular masses of bioagent identifying amplicons, each indexed to said oligonucleotide primer pair and a Staphylococcus aureus bioagent, wherein a match between said determined molecular mass and one of said plurality of molecular masses identifies, determines one or more characteristic of, or detects said Staphylococcus aureus bioagent in said sample.
 23. The method of claim 21 further comprising calculating a base composition of said at least one amplification product using said molecular mass.
 24. The method of claim 23 further comprising comparing said calculated base composition to a database comprising a plurality of base compositions of bioagent identifying amplicons, each indexed to said oligonucleotide primer pair and a Staphylococcus aureus bioagent, wherein a match between said calculated base composition and a base composition in said database identifies, determines one or more characteristics of, or detects said Staphylococcus aureus bioagent in said sample.
 25. The method of claim 21 wherein said forward primer comprises at least 70% sequence identity with SEQ ID NO:
 318. 26. The method of claim 21 wherein said reverse primer comprises at least 70% sequence identity with SEQ ID NO:
 1300. 27. The method of claim 21 further comprising repeating said amplifying and determining steps using at least one additional oligonucleotide primer pair designed to hybridize to a Staphylococcus aureus gene encoding arcC, aroE, gmk, gta, yqi, tpi, or a combination thereof. 